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- PDB-6r9n: Peroxy diiron species of chemotaxis sensor ODP -

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Basic information

Entry
Database: PDB / ID: 6r9n
TitlePeroxy diiron species of chemotaxis sensor ODP
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN / chemotaxis sensor / diiron-peroxo adduct / phosphatase
Function / homologyODP family beta lactamase / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / : / OXYGEN ATOM / PEROXIDE ION / Lactamase_B domain-containing protein
Function and homology information
Biological speciesTreponema denticola ATCC 35404 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.074 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
DepositionApr 3, 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,15311
Polymers57,7982
Non-polymers3559
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-86 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.675, 85.451, 118.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 28899.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35404 (bacteria)
Gene: HMPREF9721_01162 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2CWM4

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.16 Å3/Da / Density % sol: 42.95 % / Description: Thin sheets
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% Polyethyleneglycol 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.074→42.73 Å / Num. obs: 27969 / % possible obs: 98.59 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0513 / Rrim(I) all: 0.07254 / Net I/σ(I): 12.14
Reflection shellResolution: 2.074→2.148 Å / Rmerge(I) obs: 0.6203 / Num. unique obs: 2448 / CC1/2: 0.554 / % possible all: 87.12

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.074→42.73 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2387 --
Rwork0.1905 --
obs-27964 98.59 %
Displacement parametersBiso mean: 35.84 Å2
Refinement stepCycle: LAST / Resolution: 2.074→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 11 166 3884

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