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- PDB-2wfb: High resolution structure of the apo form of the orange protein (... -

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Basic information

Entry
Database: PDB / ID: 2wfb
TitleHigh resolution structure of the apo form of the orange protein (ORP) from Desulfovibrio gigas
ComponentsPUTATIVE UNCHARACTERIZED PROTEIN ORP
KeywordsBIOSYNTHETIC PROTEIN / MIXED MOLYBDENUM-COPPER SULPHIDE CLUSTER / ALPHA AND BETA PROTEIN
Function / homology
Function and homology information


Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Uncharacterized protein orp
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNajmudin, S. / Bonifacio, C. / Duarte, A.G. / Pereira, A.S. / Moura, I. / Moura, J.M. / Romao, M.J.
Citation
Journal: To be Published
Title: High Resolution Crystal Structure of the Apo Form of the Orange Protein (Apo-Orp) from Desulfovibrio Gigas
Authors: Najmudin, S. / Bonifacio, C. / Duarte, A.G. / Moura, I. / Moura, J.G. / Romao, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Crystallographic Analysis of the Apo Form of the Orange Protein (Orp) from Desulfovibrio Gigas.
Authors: Najmudin, S. / Bonifacio, C. / Duarte, A.G. / Pauleta, S.R. / Moura, I. / Moura, J.J.G. / Romao, M.J.
History
DepositionApr 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE UNCHARACTERIZED PROTEIN ORP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4565
Polymers12,1121
Non-polymers3444
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.078, 43.078, 106.085
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2075-

HOH

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Components

#1: Protein PUTATIVE UNCHARACTERIZED PROTEIN ORP / THE ORANGE PROTEIN


Mass: 12111.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO GIGAS (bacteria) / Plasmid: PET 21-D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5DUA6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST THREE RESIDUES (ASH) ARE A RECOMBINANT ARTIFACT, I.E. ACTUAL LENGTH OF PROTEIN IS 117 AMINO ...FIRST THREE RESIDUES (ASH) ARE A RECOMBINANT ARTIFACT, I.E. ACTUAL LENGTH OF PROTEIN IS 117 AMINO ACID RESIDUES.

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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: 2.08 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 4.5
Details: 0.1 M NA ACETATE, 0.2 M NAH2PO4 PH 4.5, 15-30% PEG 3K OR PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→106 Å / Num. obs: 7446 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 16.9 / % possible all: 62.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0036refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O13

1o13


Resolution: 2→106 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.182 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24448 347 4.7 %RANDOM
Rwork0.18278 ---
obs0.18585 7108 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 19 78 947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022890
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9751209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2525123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5824.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69515134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.366155
X-RAY DIFFRACTIONr_chiral_restr0.140.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021677
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.5596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5512934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6563294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5614.5273
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 20 -
Rwork0.193 328 -
obs--58 %

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