4HCC | pdb_00004hcc

The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex

PDB DOI: https://doi.org/10.2210/pdb4HCC/pdb
NAKB: 4HCC

Classification: HYDROLASE/DNA
Organism(s): Escherichia coli DH5[alpha]
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-29 Released: 2013-10-09
Deposition Author(s): Qiu, R., Wei, J., Lou, T., Liu, M., Ji, C., Gong, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.185 (Depositor), 0.182 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structures of Escherichia coli exonuclease I in complex with the single strand DNA

Qiu, R., Lou, T., Wei, J., Liu, M., Gu, S., Tang, R., Ji, C., Gong, W.

To be published.

Macromolecule Content

Total Structure Weight: 119.36 kDa
Atom Count: 8,059
Modeled Residue Count: 948
Deposited Residue Count: 986
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease I	A, B	481	Escherichia coli DH5[alpha]	Mutation(s): 0 Gene Names: b2011, cpeA, JW1993, sbcB, xonA EC: 3.1.11.1
UniProt
Find proteins for P04995 (Escherichia coli (strain K12)) Explore P04995 Go to UniProtKB: P04995
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04995
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(APAPAPAPAPAPAPAPAPAPAPA)-3')	C, D	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C]	Q [auth C], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain Q [auth C] Focus chain R [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B], P [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.245 (Depositor), 0.245 (DCC)
R-Value Work: 0.185 (Depositor), 0.182 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.037	α = 90
b = 108.692	β = 90
c = 158.403	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-09
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description