1gk9

From PDBWiki

Authors	McVey, C.E. Walsh, M.A. Dodson, G.G. Wilson, K.S. Brannigan, J.A.
Citation	Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism.
Release date	2003-04-01
Exp. Method	X-RAY DIFFRACTION
Resolution	1.3 Å
Classification	ANTIBIOTIC RESISTANCE

Sequence

Chain A (260 residues): Blast Uniprot EC 3.5.1.11

EQSSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRA
QIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLT
ALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTAALLPRYDLPAPMLDRPAKGADGALLALAAGK
NRETIAAQFAQGGANGLAGY

Chain B (557 residues): Blast Uniprot EC 3.5.1.11

SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAE
RLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKA
KNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANW
NNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLV
ETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAV
QGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRG
TENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR

User comments

Zero ocuppancy for some atoms

Source: [1]

Residues: 60, 200, 432, 436 have one/more atoms with occupancy "0.00"

ATOM    495  CE  LYS A  60      -8.610  -9.509  23.600  0.00 63.89         C
ATOM    496  NZ  LYS A  60      -8.812  -8.566  22.504  0.00 72.26         N

There are 2 possibilities here:

• this is simply a format error
• they should be unobserved. If this is the case then this practice is not ideal because most molecular viewers would display these atoms without noticing the ocuppancy field.

Querying the whole PDB it seems that it's not totally unusual: around 4 million atom records (i.e. ~1% of total) have 0 occupancy.

See also 1h4x.

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