3M4C

A Zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase

PDB DOI: https://doi.org/10.2210/pdb3M4C/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-03-10 Released: 2011-01-12
Deposition Author(s): Tezcan, F.A., Ni, T.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural characterization of a microperoxidase inside a metal-directed protein cage.

Ni, T.W., Tezcan, F.A.

(2010) Angew Chem Int Ed Engl 49: 7014-7018

PubMed: 20721993 Search on PubMed
DOI: https://doi.org/10.1002/anie.201001487
Primary Citation of Related Structures:
3M15, 3M4B, 3M4C

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0356, La Jolla, CA 92093, USA.

Macromolecule Content

Total Structure Weight: 51.56 kDa
Atom Count: 4,011
Modelled Residue Count: 433
Deposited Residue Count: 433
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C, D	106	Escherichia coli	Mutation(s): 13 Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-Peptide Fragment	E	9	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E]	F [auth A], K [auth B], R [auth C], T [auth D], X [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain X [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D]	H [auth A] I [auth A] J [auth A] M [auth B] N [auth B] H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], V [auth D], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth D] Focus chain W [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain S [auth D] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] MOL2 format, chain U [auth D]	G [auth A], L [auth B], S [auth D], U [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.190
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.892	α = 90
b = 126.892	β = 90
c = 167.944	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Tezcan, F.A.

Ni, T.W.

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-09-18
Changes: Derived calculations
Version 1.3: 2021-10-06
Changes: Database references, Derived calculations, Source and taxonomy

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Help and Resources

3M4C

A Zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase

Structural characterization of a microperoxidase inside a metal-directed protein cage.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2