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- PDB-2pve: NMR and X-ray Analysis of Structural Additivity in Metal Binding ... -

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Basic information

Entry
Database: PDB / ID: 2pve
TitleNMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / ultrahigh resolution
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
ACETATE ION / Rubredoxin
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.79 Å
AuthorsLeMaster, D.M. / Anderson, J.S. / Wang, L. / Guo, Y. / Li, H. / Hernandez, G.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin.
Authors: Lemaster, D.M. / Anderson, J.S. / Wang, L. / Guo, Y. / Li, H. / Hernandez, G.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,67210
Polymers18,2363
Non-polymers4357
Water5,116284
1
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2624
Polymers6,0791
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2063
Polymers6,0791
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2033
Polymers6,0791
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.169, 56.860, 38.170
Angle α, β, γ (deg.)90.00, 112.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rubredoxin / Rd


Mass: 6078.698 Da / Num. of mol.: 3 / Mutation: K7T,I8V,I41L,A44V,P45G,S47D,E48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pET 3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00268
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.8577
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2005 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8577 Å / Relative weight: 1
ReflectionResolution: 0.79→22 Å / Num. obs: 147089 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 27
Reflection shellResolution: 0.79→0.82 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.197 / % possible all: 36.7

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Processing

Software
NameClassification
CBASSdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C09

1c09


Resolution: 0.79→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.125 -5 %RANDOM
all0.112 145421 --
obs0.112 -90 %-
Displacement parametersBiso mean: 11.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.08 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.36 Å
Refinement stepCycle: LAST / Resolution: 0.79→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 19 298 2806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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