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- PDB-2rdv: RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRY... -

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Basic information

Entry
Database: PDB / ID: 2rdv
TitleRUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSFER / RUBREDOXIN / COMPND / ELECTRON TRANSFER PROTEIN / METALLOPROTEIN / SULFATE-REDUCING BACTERIUM
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHiguchi, Y. / Yasuoka, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.
Authors: Misaki, S. / Morimoto, Y. / Ogata, M. / Yagi, T. / Higuchi, Y. / Yasuoka, N.
#1: Journal: Protein Pept.Lett. / Year: 1998
Title: Preliminary Crystallographic Study of Two Crystal Forms of Rubredoxin from Sulfate-Reducing Bactrium
Authors: Higuchi, Y. / Sugiyama, M.S. / Morimoto, S. / Ogata, Y. / Yagi, M. / Yasuoka, T.
History
DepositionOct 7, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUBREDOXIN
B: RUBREDOXIN
C: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9746
Polymers16,8073
Non-polymers1683
Water1,54986
1
A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6582
Polymers5,6021
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6582
Polymers5,6021
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6582
Polymers5,6021
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.300, 44.900, 51.200
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.541, 0.84, 0.023), (-0.84, -0.542, 0.027), (0.036, -0.005, 0.999)8.028, 3.198, -34.31
2given(-0.502, -0.864, -0.03), (0.864, -0.503, 0.007), (-0.021, -0.022, 1)8.87, -5.096, -16.953

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Components

#1: Protein RUBREDOXIN


Mass: 5602.237 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: IAM 12604
Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P15412
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7 / Method: microdialysis / Details: Higuchi, Y., (1998) Protein Pept.Lett., 5, 175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
250 mMTris-HCl11
360-70 %satammonium sulfate11
475-80 %satammonium sulfate12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 53316 / % possible obs: 82.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.111
Reflection
*PLUS
Num. obs: 9604 / Observed criterion σ(I): 3 / Num. measured all: 53316

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
FSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RDV

1rdv


Resolution: 1.9→20 Å / Isotropic thermal model: RESTRAINED / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.216 -5 %RANDOM
Rwork0.175 ---
obs0.175 9604 82.5 %-
Displacement parametersBiso mean: 14.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 3 86 1262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.807
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.633
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.633

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