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- PDB-1mqv: Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas... -

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Basic information

Entry
Database: PDB / ID: 1mqv
TitleCrystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / Four-Helix Bundle
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLee, J.C. / Engman, K.C. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural Features of Cytochrome c' Folding Intermediates Revealed by Fluorescence Energy-Transfer Kinetics
Authors: Lee, J.C. / Engman, K.C. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4274
Polymers26,1902
Non-polymers1,2372
Water4,774265
1
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7142
Polymers13,0951
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7142
Polymers13,0951
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.839, 62.085, 113.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C'


Mass: 13095.089 Da / Num. of mol.: 2 / Mutation: Q1A, F32W, W72F
Source method: isolated from a genetically manipulated source
Details: The protein is in the OXIDIZED (FE(III)) STATE.
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P00149
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoir
350 mM1reservoirpH6.0NaCl
410 mMsodium phosphate1droppH6.0
528 mM1dropNaCl
2PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 24, 2002
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 23685 / Num. obs: 23607 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 24.8
Reflection shellResolution: 1.78→1.81 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.487 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A7V

1a7v


Resolution: 1.78→42 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1141 -RANDOM
Rwork0.214 ---
all0.22 23685 --
obs0.214 23607 98.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.78→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 86 265 2153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shellResolution: 1.78→1.84 Å / Rfactor Rfree error: 0.043
RfactorNum. reflection% reflection
Rfree0.459 113 -
Rwork0.365 --
obs-2145 5 %
Refinement
*PLUS
Lowest resolution: 42 Å / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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