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- PDB-6juw: BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1... -

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Basic information

Entry
Database: PDB / ID: 6juw
TitleBOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / Cytochrome c oxidase membrane protein respiratory enzyme heme protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / : / : ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / : / : / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
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 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 / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c 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 VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / 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 III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / 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 / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShimada, A. / Muramoto, K. / Shinzawa-Itoh, K. / Yoshikawa, S. / Tsukihara, T.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: X-ray structures of catalytic intermediates of cytochromecoxidase provide insights into its O2activation and unidirectional proton-pump mechanisms.
Authors: Shimada, A. / Etoh, Y. / Kitoh-Fujisawa, R. / Sasaki, A. / Shinzawa-Itoh, K. / Hiromoto, T. / Yamashita, E. / Muramoto, K. / Tsukihara, T. / Yoshikawa, S.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,577184
Polymers404,29326
Non-polymers48,284158
Water45,2002509
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, X-ray structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.217, 204.650, 177.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P68530
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29725.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P00415
#4: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 16913.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 12083.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B / Cytochrome c oxidase polypeptide VIa


Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P00428
#7: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9532.667 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 9411.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc


Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6553.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P07470
#11: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 5442.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5362.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4738.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Bovine / Tissue: Heart / References: UniProt: P10175

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Sugars , 1 types, 25 molecules

#18: Sugar...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 15 types, 2642 molecules

#14: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#19: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#20: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#21: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#22: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: C2H6O2
#23: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cu2
#24: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H40O5
#25: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#26: Chemical
ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE


Mass: 768.055 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2509 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.03 Å3/Da / Density % sol: 69.5 % / Description: rectangular plate
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG 4000, Sodium phosphate buffer

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→136.1 Å / Num. obs: 606209 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 29.28 Å2 / CC1/2: 0.877 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.027 / Net I/σ(I): 38.5
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 19429 / Rpim(I) all: 0.409 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1A

5b1a


Resolution: 1.8→39.876 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 30337 5.02 %
Rwork0.1565 --
obs0.1582 604925 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28510 0 2939 2509 33958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232679
X-RAY DIFFRACTIONf_angle_d1.84343924
X-RAY DIFFRACTIONf_dihedral_angle_d14.15819182
X-RAY DIFFRACTIONf_chiral_restr0.1124638
X-RAY DIFFRACTIONf_plane_restr0.0125153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.29919790.256918783X-RAY DIFFRACTION98
1.8205-1.84190.26339750.239119103X-RAY DIFFRACTION100
1.8419-1.86430.247810160.224318938X-RAY DIFFRACTION99
1.8643-1.88790.269210.219619098X-RAY DIFFRACTION100
1.8879-1.91280.24429260.207819124X-RAY DIFFRACTION100
1.9128-1.9390.22829980.194419039X-RAY DIFFRACTION100
1.939-1.96670.214910320.186519058X-RAY DIFFRACTION100
1.9667-1.9960.20899950.177718996X-RAY DIFFRACTION100
1.996-2.02720.209410150.177319157X-RAY DIFFRACTION100
2.0272-2.06050.21229610.171919040X-RAY DIFFRACTION100
2.0605-2.0960.19389810.163619137X-RAY DIFFRACTION100
2.096-2.13410.17729810.157619158X-RAY DIFFRACTION100
2.1341-2.17510.187810030.157319073X-RAY DIFFRACTION100
2.1751-2.21950.190910130.156719131X-RAY DIFFRACTION100
2.2195-2.26780.193810270.157519063X-RAY DIFFRACTION100
2.2678-2.32050.187710400.149919068X-RAY DIFFRACTION100
2.3205-2.37860.180810160.15419124X-RAY DIFFRACTION100
2.3786-2.44290.179410530.14919138X-RAY DIFFRACTION100
2.4429-2.51470.185810190.150319149X-RAY DIFFRACTION100
2.5147-2.59590.19210130.151319186X-RAY DIFFRACTION100
2.5959-2.68870.17210180.14919188X-RAY DIFFRACTION100
2.6887-2.79630.185410110.155119223X-RAY DIFFRACTION100
2.7963-2.92350.186910080.156819206X-RAY DIFFRACTION100
2.9235-3.07760.195710640.155919221X-RAY DIFFRACTION100
3.0776-3.27030.18710110.15619285X-RAY DIFFRACTION100
3.2703-3.52270.185710520.15219263X-RAY DIFFRACTION100
3.5227-3.87690.180410760.146319302X-RAY DIFFRACTION100
3.8769-4.43730.164910360.136619387X-RAY DIFFRACTION100
4.4373-5.58810.164110910.135619419X-RAY DIFFRACTION100
5.5881-39.8760.211410060.172819531X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3010.0326-0.10570.1589-0.03170.28720.01060.06680.02040.00440.01240.01480.0232-0.04730.00090.13160.0068-0.00980.13430.01680.105561.2378306.832197.3342
20.40210.1130.00880.2439-0.03650.37120.03120.1136-0.09830.0180.0147-0.0992-0.04420.0720.11570.1286-0.0097-0.00470.1177-0.03380.1995126.5387313.0188193.867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1 through 514) or (chain B and resid 1 through 227) or (chain C and resid 3 through 261) or (chain D) or (chain E) or (chain F and resid 1 through 98) or (chain G) or (chain H) or (chain I) or (chain J) or (chain K) or (chain L) or (chain M)
2X-RAY DIFFRACTION2(chain N and resid 1 through 514) or (chain O and resid 1 through 227) or (chain P and resid 3 through 261) or (chain Q) or (chain R) or (chain S and resid 1 through 98) or (chain T) or (chain U) or (chain V) or (chain W) or (chain X) or (chain Y) or (chain Z)

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