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- PDB-1mdv: KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILI... -

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Basic information

Entry
Database: PDB / ID: 1mdv
TitleKEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / MUTANT CYTOCHROME C3 / DESULFOVIBRIO VULGARIS HILDENBOROUGH
Function / homology
Function and homology information


anaerobic respiration / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDolla, A. / Arnoux, P. / Protasevich, I. / Lobachov, V. / Brugna, M. / Guidici-Orticoni, M.T. / Haser, R. / Czjzek, M. / Makarov, A. / Brushi, M.
Citation
Journal: Biochemistry / Year: 1999
Title: Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies.
Authors: Dolla, A. / Arnoux, P. / Protasevich, I. / Lobachov, V. / Brugna, M. / Giudici-Orticoni, M.T. / Haser, R. / Czjzek, M. / Makarov, A. / Bruschi, M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure Analysis of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.9 A Resolution
Authors: Matias, P.M. / Frazao, C. / Morais, J. / Coll, M. / Carrondo, M.A.
#2: Journal: J.Biochem.(Tokyo) / Year: 1991
Title: Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 2 A Resolution
Authors: Morimoto, Y. / Tani, T. / Okumura, H. / Higuchi, Y. / Yasuoka, N.
History
DepositionSep 8, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn_type.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 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,23910
Polymers23,3072
Non-polymers4,9328
Water1,928107
1
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1195
Polymers11,6531
Non-polymers2,4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1195
Polymers11,6531
Non-polymers2,4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,95540
Polymers93,2288
Non-polymers19,72832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area50060 Å2
ΔGint-873 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.220, 97.220, 36.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6631, 0.74515, -0.07111), (0.74853, 0.66028, -0.06107), (0.00145, -0.09372, -0.9956)
Vector: 7.97559, -3.76682, 14.71943)

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Components

#1: Protein CYTOCHROME C3 / TETRA HEME CYTOCHROME / CYTOCHROME C3 (MR 13000)


Mass: 11653.446 Da / Num. of mol.: 2 / Mutation: F20L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Cellular location: PERIPLASMIC / Gene: CYC / Plasmid: PJRC800F20L / Cellular location (production host): PERIPLASM / Gene (production host): CYC / Production host: Desulfovibrio desulfuricans (bacteria) / Strain (production host): G200 / References: UniProt: P00131
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.91 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
240 mMTris-HCl1drop
33.0-3.4 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→23 Å / Num. obs: 14381 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 38.53 Å2 / Rsym value: 0.063 / Net I/σ(I): 16.4
Reflection shellResolution: 2.3→2.35 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.505 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 48916 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 93.2 % / Num. unique obs: 946 / Rmerge(I) obs: 0.505

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTH

1cth
PDB Unreleased entry


Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: THE MUTATION F20L AFFECTS THE N-TERMINAL PART OF THE MOLECULE. OCCUPANCIES WERE ARBITRARILY SET TO 0.3 FOR BADLY DEFINED RESIDUES. SOME MORE RESIDUES ON THE SURFACE WERE ALSO NOT DEFINED IN ...Details: THE MUTATION F20L AFFECTS THE N-TERMINAL PART OF THE MOLECULE. OCCUPANCIES WERE ARBITRARILY SET TO 0.3 FOR BADLY DEFINED RESIDUES. SOME MORE RESIDUES ON THE SURFACE WERE ALSO NOT DEFINED IN THE ELECTRON DENSITY AND THEIR OCCUPANCIES EQUALLY SET TO 0.3.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1367 10 %RANDOM
Rwork0.224 ---
obs0.224 13817 88.4 %-
Displacement parametersBiso mean: 43.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.403 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 344 107 1981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.361
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
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.348 140
Rwork0.313 1325
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19X.HEMETOPHCSDX.PRO
X-RAY DIFFRACTION3TOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.283
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.361

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