3C37 | pdb_00003c37

X-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A. Northeast Structural Genomics Consortium target GsR143A

PDB DOI: https://doi.org/10.2210/pdb3C37/pdb

Classification: HYDROLASE
Organism(s): Geobacter sulfurreducens PCA
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-27 Released: 2008-02-12
Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Vorobiev, S.M., Forouhar, F., Wang, D., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.254 (Depositor), 0.259 (DCC)
R-Value Work:
0.219 (Depositor), 0.221 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

X-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A.

Kuzin, A.P., Chen, Y., Seetharaman, J., Vorobiev, S.M., Forouhar, F., Wang, D., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 58.16 kDa
Atom Count: 3,822
Modeled Residue Count: 445
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, M48 family	A, B	253	Geobacter sulfurreducens PCA	Mutation(s): 0 Gene Names: GSU1437
UniProt
Find proteins for Q74D82 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74D82 Go to UniProtKB: Q74D82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q74D82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.254 (Depositor), 0.259 (DCC)
R-Value Work: 0.219 (Depositor), 0.221 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.84	α = 88.07
b = 44.613	β = 75.18
c = 71.772	γ = 65.64

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Refinement description, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary