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- PDB-2hqv: X-ray Crystal Structure of Protein AGR_C_4470 from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2hqv
TitleX-ray Crystal Structure of Protein AGR_C_4470 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR92.
ComponentsAGR_C_4470p
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / AtR92 / AGR_C_4470 / Q7CX01_AGRT5 / 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 speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVorobiev, S.M. / Neely, H. / Seetharaman, J. / Zhao, L. / Cunningham, K. / Ma, L.C. / Fang, Y. / Xiao, R. / Acton, T. / Montelione, T.G. ...Vorobiev, S.M. / Neely, H. / Seetharaman, J. / Zhao, L. / Cunningham, K. / Ma, L.C. / Fang, Y. / Xiao, R. / Acton, T. / Montelione, T.G. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: 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
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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: AGR_C_4470p


Theoretical massNumber of molelcules
Total (without water)21,6211
Polymers21,6211
Non-polymers00
Water1,20767
1
A: AGR_C_4470p

A: AGR_C_4470p


Theoretical massNumber of molelcules
Total (without water)43,2412
Polymers43,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)66.239, 72.322, 104.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsDimer. The second part of the dimer is generated by -X, -Y, Z + (1 0 0) operator.

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Components

#1: Protein AGR_C_4470p


Mass: 21620.748 Da / Num. of mol.: 1 / Mutation: C-tag: LEHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58-ATCC 33970 / Gene: AGR_C_4470 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q7CX01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% PEG 400, 0.1M Magnesium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97960, 0.97923, 0.97947, 0.96783
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.979231
30.979471
40.967831
ReflectionResolution: 2→30 Å / Num. all: 32944 / Num. obs: 32911 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→29.76 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 109456.86 / 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 REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1201 4 %RANDOM
Rwork0.241 ---
obs0.241 29683 90.3 %-
all-31917 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.1963 Å2 / ksol: 0.368725 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--8.28 Å20 Å20 Å2
2---3.91 Å20 Å2
3---12.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.08 Å
Refinement stepCycle: LAST / Resolution: 2→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 67 1333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 178 4.3 %
Rwork0.241 3915 -
obs--74.9 %
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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