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- PDB-6qwo: Zinc-reconstituted ODP from T. maritima -

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Basic information

Entry
Database: PDB / ID: 6qwo
TitleZinc-reconstituted ODP from T. maritima
ComponentsOxygen-binding diiron protein
KeywordsSIGNALING PROTEIN / chemotaxis sensor / diiron-peroxo adduct / phosphatase
Function / homologyODP domain / ODP family beta lactamase / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Lactamase_B domain-containing protein / Lactamase_B domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMuok, A.R. / Crane, B.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR35GM122535 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 RR029205 United States
National Science Foundation (United States)2014155468 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species.
Authors: Muok, A.R. / Deng, Y. / Gumerov, V.M. / Chong, J.E. / DeRosa, J.R. / Kurniyati, K. / Coleman, R.E. / Lancaster, K.M. / Li, C. / Zhulin, I.B. / Crane, B.R.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxygen-binding diiron protein
B: Oxygen-binding diiron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6636
Polymers58,4012
Non-polymers2624
Water5,314295
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-183 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.433, 121.709, 159.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

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Components

#1: Protein Oxygen-binding diiron protein


Mass: 29200.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: Tmari_0010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4NP31, UniProt: Q9S5W7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 30% polyethyleneglycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→23.22 Å / Num. all: 31055 / Num. obs: 59080 / % possible obs: 99.84 % / Redundancy: 10.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.041 / Rrim(I) all: 0.149 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.656 / Num. unique obs: 3052 / CC1/2: 0.887 / Rpim(I) all: 0.222 / Rrim(I) all: 0.793

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2→23.22 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2093 --
Rwork0.1648 --
obs-31043 99.84 %
Refinement stepCycle: LAST / Resolution: 2→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 4 295 4409

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