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- PDB-4bmw: Crystal structure of the Streptomyces reticuli HbpS E78D, E81D do... -

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Basic information

Entry
Database: PDB / ID: 4bmw
TitleCrystal structure of the Streptomyces reticuli HbpS E78D, E81D double mutant
ComponentsEXTRACELLULAR HAEM-BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / OXIDATIVE STRESS / IRON BINDING / HEME
Function / homology
Function and homology information


Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular haem-binding protein
Similarity search - Component
Biological speciesSTREPTOMYCES RETICULI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWagener, S. / Kursula, I. / Wedderhoff, I. / Groves, M.R. / Ortiz de Orue Lucana, D.
CitationJournal: Plos One / Year: 2013
Title: Iron Binding at Specific Sites within the Octameric Hbps Protects Streptomycetes from Iron-Mediated Oxidative Stress.
Authors: Wedderhoff, I. / Kursula, I. / Groves, M.R. / Ortiz de Orue Lucana, D.
History
DepositionMay 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Data collection
Revision 1.2Jul 15, 2015Group: Data collection
Revision 1.3Feb 7, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation_author / diffrn_source / entity_src_gen
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site ..._citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXTRACELLULAR HAEM-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,4861
Polymers15,4861
Non-polymers00
Water2,000111
1
A: EXTRACELLULAR HAEM-BINDING PROTEIN
x 8


Theoretical massNumber of molelcules
Total (without water)123,8898
Polymers123,8898
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_735-y+2,x-2,z1
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation2_955-x+4,-y,z1
crystal symmetry operation5_954-x+4,y,-z-11
crystal symmetry operation8_774-y+2,-x+2,-z-11
crystal symmetry operation4_775y+2,-x+2,z1
crystal symmetry operation7_734y+2,x-2,-z-11
Buried area20140 Å2
ΔGint-94.4 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.390, 77.390, 79.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-15-

PRO

21A-2015-

HOH

31A-2027-

HOH

41A-2028-

HOH

51A-2031-

HOH

61A-2036-

HOH

71A-2093-

HOH

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Components

#1: Protein EXTRACELLULAR HAEM-BINDING PROTEIN / HBPS


Mass: 15486.170 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES RETICULI (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9RIM2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 8.3
Details: 20% (W/V) POLYETHYLENE GLYCOL 3350 AND 0.2 M TRI-POTASSIUM CITRATE, pH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 8579 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 29.68 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.84 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPV
Resolution: 1.99→54.723 Å / SU ML: 0.22 / σ(F): 2.01 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 429 5 %
Rwork0.1824 --
obs0.1849 8576 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 1.99→54.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 111 1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041080
X-RAY DIFFRACTIONf_angle_d0.8271478
X-RAY DIFFRACTIONf_dihedral_angle_d13.77386
X-RAY DIFFRACTIONf_chiral_restr0.047171
X-RAY DIFFRACTIONf_plane_restr0.003202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.2780.33341370.26912651X-RAY DIFFRACTION100
2.278-2.870.24041410.21752699X-RAY DIFFRACTION100
2.87-54.74370.20541510.14932797X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.76641.10220.27921.7592-0.9522.10890.3596-0.98780.39081.3087-0.348-0.3089-0.04960.02650.14640.4804-0.1083-0.04730.281-0.00040.2095167.4679-28.3919-21.8363
29.16718.1585-6.76219.6681-7.40696.7041-0.4720.6532-0.89730.77760.4479-0.65480.0882-0.64550.15020.42430.09130.04280.2837-0.0290.3368175.6089-23.4007-39.9085
32.4292-0.35281.41653.1084-4.22127.22090.10710.11090.12030.6895-0.7895-0.918-0.41980.69780.73870.2925-0.0448-0.040.37410.02480.3355185.7054-0.5354-46.1978
41.38540.02670.91184.4397-0.37852.1759-0.07840.03520.17150.25480.0388-0.2593-0.44020.270.04540.2252-0.03880.02850.3012-0.01980.2138175.53711.3344-46.9126
55.68062.2644-0.3882.86282.7724.57740.02220.2705-0.1250.0632-0.03110.6832-0.0227-0.1724-0.01150.2540.0261-0.01330.29430.02020.2518169.13-3.8503-50.3617
68.7576-0.57842.46282.7735-4.45417.3380.28580.9983-0.2612-0.6874-0.03280.25890.8136-0.2883-0.28750.3753-0.05130.01110.3448-0.09760.2576165.241-8.2198-62.0343
72.58620.41060.88653.6479-0.62694.05630.00630.1209-0.15890.02590.01130.08440.142-0.1328-0.0270.2709-0.00930.03340.2328-0.02220.1883173.1445-6.7458-53.7019
89.7525-3.31335.76335.6199-5.93936.93620.31680.49760.2461-1.1679-0.3319-0.8960.69890.47890.03840.37570.0110.07440.3652-0.03290.3091182.7029-3.0703-56.3218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 11 THROUGH 19 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 20 THROUGH 30 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 31 THROUGH 47 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 48 THROUGH 75 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 76 THROUGH 90 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 91 THROUGH 109 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 110 THROUGH 139 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 140 THROUGH 156 )

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