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- PDB-1gqa: Cytochrome c' from Rhodobacter Spheriodes -

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Basic information

Entry
Database: PDB / ID: 1gqa
TitleCytochrome c' from Rhodobacter Spheriodes
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HEME
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / 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 speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKantardjieff, K.A. / Rupp, B.
CitationJournal: J.Chem.Cryst. / Year: 2003
Title: High Resolution Crystal Structure of Ferricytochrome C' from Rhodobacter Sphaeroides
Authors: Ramirez, L.M. / Axelrod, H.L. / Herron, S.R. / Rupp, B. / Allen, J.P. / Kantardjieff, K.A.
History
DepositionNov 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / struct_biol
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_starting_model
Revision 1.5Dec 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_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.status_code_sf / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0894
Polymers26,8522
Non-polymers1,2372
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.100, 48.100, 115.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.508819, 0.860871, 0.002075), (0.860576, 0.508705, -0.025043), (-0.022615, -0.010957, -0.999684)
Vector: 71.5396, -2.8482, -113.4344)

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Components

#1: Protein CYTOCHROME C' / FERRICYTOCHROME C'


Mass: 13426.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: PERIPLASMICPeriplasm / References: UniProt: P00148
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE 2 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE(S) : RESIDUE GLY 117 ...THERE ARE 2 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE(S) : RESIDUE GLY 117 (THR IN THE P00148 ENTRY) AND RESIDUE THR 118 (GLY IN THE P00148 ENTRY) APPEAR TO SWAPPED. FROM THE ELECTRON DENSITY IT IS EVIDENT THAT RESIDUE 117 IS IN FACT GLY AND 118 IS THERONINE

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: 12MG/ML, 5+5 UL HANGING DROP, NA-ACETATE 25MM PH4.5, PEG 8000 15%, pH 4.50
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMsodium phosphate1droppH4.5
320 %(w/v)PEG80001reservoir
450 mMsodium phosphate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→31 Å / Num. obs: 24077 / % possible obs: 86.5 % / Redundancy: 2.8 % / Rsym value: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.16 / % possible all: 56.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 31 Å / % possible obs: 87 % / Num. measured all: 67416 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 57 % / Num. unique obs: 2553 / Num. measured obs: 5617 / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPQ

1cpq


Resolution: 1.8→25 Å / SU B: 5.276 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25374 2408 10 %RANDOM
Rwork0.2045 ---
obs0.20948 21666 86.6 %-
Displacement parametersBiso mean: 24.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 86 291 2263
Refinement
*PLUS
Lowest resolution: 31 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.745
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rfactor Rfree: 0.351 / Rfactor Rwork: 0.271

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