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- PDB-2ph0: Crystal structure of the Q6D2T7_ERWCT protein from Erwinia caroto... -

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Basic information

Entry
Database: PDB / ID: 2ph0
TitleCrystal structure of the Q6D2T7_ERWCT protein from Erwinia carotovora. NESG target EwR41.
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q6D2T7 / ERWCT / NESG / EwR41 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyIntracellular heme transport protein HutX-like / Haem utilisation ChuX/HutX / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / : / 3-Layer(aba) Sandwich / Alpha Beta / Heme utilization cystosolic carrier protein HutX
Function and homology information
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsVorobiev, S.M. / Neely, H. / Seetharaman, J. / Chen, C.-X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T. ...Vorobiev, S.M. / Neely, H. / Seetharaman, J. / Chen, C.-X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Crystal structure of the Q6D2T7_ERWCT protein from Erwinia carotovora.
Authors: Vorobiev, S.M. / Neely, H. / Seetharaman, J. / Chen, C.-X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L.
#1: Journal: Protein Sci. / Year: 2007
Title: Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens.
Authors: Vorobiev, S.M. / Neely, H. / Seetharaman, J. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,1532
Polymers39,1532
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.584, 38.736, 58.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 19576.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Strain: SCRI 1043 / Gene: ECA3008 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6D2T7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.61 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: 40% PEG 1000, 0.1M Ammonium nitrate, 0.1M MOPS, pH 7.0, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 49308 / Num. obs: 49308 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.38
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.39 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→43.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 134975.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2290 4.9 %RANDOM
Rwork0.219 ---
obs0.219 46417 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.7962 Å2 / ksol: 0.350374 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---5.27 Å20 Å2
3---3.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 0 224 2671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.64
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 293 4.3 %
Rwork0.232 6464 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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