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- PDB-1ocr: BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE -

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Basic information

Entry
Database: PDB / ID: 1ocr
TitleBOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE
Components(CYTOCHROME C ...) x 13
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN) / CYTOCHROME C OXIDASE / REDUCED
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like
Similarity search - Domain/homology
COPPER (II) ION / HEME-A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C ...COPPER (II) ION / HEME-A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å
AuthorsTsukihara, T. / Yao, M.
Citation
Journal: Science / Year: 1998
Title: Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.
Authors: Yoshikawa, S. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yamashita, E. / Inoue, N. / Yao, M. / Fei, M.J. / Libeu, C.P. / Mizushima, T. / Yamaguchi, H. / Tomizaki, T. / Tsukihara, T.
#1: Journal: Science / Year: 1996
Title: The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A
Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S.
#2: Journal: Science / Year: 1995
Title: Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A
Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S.
History
DepositionJul 7, 1998Processing site: BNL
Revision 1.0Jul 29, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 OXIDASE
B: CYTOCHROME C OXIDASE
C: CYTOCHROME C OXIDASE
D: CYTOCHROME C OXIDASE
E: CYTOCHROME C OXIDASE
F: CYTOCHROME C OXIDASE
G: CYTOCHROME C OXIDASE
H: CYTOCHROME C OXIDASE
I: CYTOCHROME C OXIDASE
J: CYTOCHROME C OXIDASE
K: CYTOCHROME C OXIDASE
L: CYTOCHROME C OXIDASE
M: CYTOCHROME C OXIDASE
N: CYTOCHROME C OXIDASE
O: CYTOCHROME C OXIDASE
P: CYTOCHROME C OXIDASE
Q: CYTOCHROME C OXIDASE
R: CYTOCHROME C OXIDASE
S: CYTOCHROME C OXIDASE
T: CYTOCHROME C OXIDASE
U: CYTOCHROME C OXIDASE
V: CYTOCHROME C OXIDASE
W: CYTOCHROME C OXIDASE
X: CYTOCHROME C OXIDASE
Y: CYTOCHROME C OXIDASE
Z: CYTOCHROME C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,65542
Polymers409,63726
Non-polymers4,01816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area119100 Å2
ΔGint-1023 kcal/mol
Surface area122830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.100, 210.500, 178.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.993679, -0.001063, 0.112252), (0.001373, -0.999995, 0.002682), (0.112249, 0.00282, 0.993676)
Vector: 170.18407, 637.43274, -10.45932)
DetailsTHIS ENZYME IS A MULTI-COMPONENT PROTEIN COMPLEX AND IS A HOMODIMER. EACH MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS: HEME A, HEME A3, CUA, CUB, MG, NA, AND ZN. THE SIDE CHAINS OF H 240 AND Y244 OF SUBUNITS A AND N ARE LINKED TOGETHER BY A COVALENT BOND. THE ELECTRON DENSITY OF REGION FROM D(Q)1 TO D(Q)3, H(U)1 TO H(U)6, J(W)59, K(X)1 TO K(X)5, K(X)55 TO K(X)56 AND M(Z)44 TO M(Z)46 IS NOISY AND VERY POOR. THOSE RESIDUES CANNOT BE MODELLED.

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Components

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CYTOCHROME C ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P68530, cytochrome-c oxidase
#3: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 29943.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00423, cytochrome-c oxidase
#5: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00426, cytochrome-c oxidase
#6: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00428, cytochrome-c oxidase
#7: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07471, cytochrome-c oxidase
#8: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00429, cytochrome-c oxidase
#9: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P04038, cytochrome-c oxidase
#10: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07470, cytochrome-c oxidase
#11: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13183, cytochrome-c oxidase
#12: Protein/peptide CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00430, cytochrome-c oxidase
#13: Protein/peptide CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. FULLY REDUCED STATE.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P10175, cytochrome-c oxidase

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Non-polymers , 5 types, 16 molecules

#14: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#17: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#18: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: OSCILLATION METHOD FOR DATA COLLECTION
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 19, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. obs: 270061 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 36.56 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.4
Reflection shellResolution: 2.35→2.46 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 72
Reflection
*PLUS
Num. measured all: 1184694
Reflection shell
*PLUS
% possible obs: 72 % / Num. unique obs: 28814 / Num. measured obs: 55541 / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TSUKISCALE (LOCAL)data reduction
X-PLOR3.84model building
X-PLOR3.84refinement
TSUKISCALE (LOCAL)data scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: MIR / Resolution: 2.35→15 Å / Rfactor Rfree error: 0.0021 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GAUSS / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 13086 5 %RANDOM
Rwork0.203 ---
obs0.203 263548 89.832 %-
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.1672 Å20 Å20 Å2
2--3.1426 Å20 Å2
3----4.3098 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-15 Å
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28578 0 252 0 28830
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.158
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.716
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 2 Å2 / Rms dev position: 300 Å
LS refinement shellResolution: 2.35→2.46 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.302 1316 3.619 %
Rwork0.288 25165 -
obs--72.83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19X.HEME
X-RAY DIFFRACTION3PARAM19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.211 / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.205
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.716

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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