7XMJ | pdb_00007xmj

Crystal structure of carbohydrate esterase family 7 acetyl xylan esterase

PDB DOI: https://doi.org/10.2210/pdb7XMJ/pdb
Entry: 7XMJ supersedes: 7CUZ

Classification: STRUCTURAL PROTEIN
Organism(s): Lactococcus lactis subsp. lactis KF147
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-26 Released: 2023-05-31
Deposition Author(s): Jiang, Z.Q., Ma, J.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.248 (Depositor), 0.250 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of carbohydrate esterase family 7 acetyl xylan esterase

Jiang, Z.Q., Ma, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 143.37 kDa
Atom Count: 10,061
Modeled Residue Count: 1,218
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylxylan esterase	A, B, C, D	312	Lactococcus lactis subsp. lactis KF147	Mutation(s): 0 Gene Names: axe, LLKF_1447 EC: 3.1.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C], G [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.248 (Depositor), 0.250 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.714	α = 90
b = 147.714	β = 90
c = 135.389	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	model building
PHENIX	refinement
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

This entry supersedes: 7CUZ

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-05-31
Type: Initial release
Version 1.1: 2023-11-08
Changes: Advisory, Data collection
Version 1.2: 2023-11-29
Changes: Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.