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- PDB-1t9o: Crystal Structure of V44G Cp Rubredoxin -

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Basic information

Entry
Database: PDB / ID: 1t9o
TitleCrystal Structure of V44G Cp Rubredoxin
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
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 speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, I.Y. / Eidsness, M.K. / Lin, I.J. / Gebel, E.B. / Youn, B. / Harley, J.L. / Machonkin, T.E. / Frederick, R.O. / Markley, J.L. / Smith, E.T. ...Park, I.Y. / Eidsness, M.K. / Lin, I.J. / Gebel, E.B. / Youn, B. / Harley, J.L. / Machonkin, T.E. / Frederick, R.O. / Markley, J.L. / Smith, E.T. / Ichiye, T. / Kang, C.
CitationJournal: Proteins / Year: 2004
Title: Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: Effects of side-chain size on reduction potential.
Authors: Park, I.Y. / Eidsness, M.K. / Lin, I.J. / Gebel, E.B. / Youn, B. / Harley, J.L. / Machonkin, T.E. / Frederick, R.O. / Markley, J.L. / Smith, E.T. / Ichiye, T. / Kang, C.
History
DepositionMay 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1966
Polymers18,0293
Non-polymers1683
Water2,828157
1
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0652
Polymers6,0101
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0652
Polymers6,0101
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0652
Polymers6,0101
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.450, 57.670, 38.630
Angle α, β, γ (deg.)90.00, 112.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rubredoxin / Rd


Mass: 6009.532 Da / Num. of mol.: 3 / Mutation: V44G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00268
#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.: 157 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 10074 / Num. obs: 9813 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.414
Reflection shellResolution: 2→2.07 Å / % possible all: 87.5

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Processing

Software
NameVersionClassification
ADSCdata collection
CrystalCleardata reduction
AMoREphasing
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.183 490 RANDOM
Rwork0.173 --
all0.177 10074 -
obs0.175 9813 -
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 3 157 1387

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