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- PDB-3h1k: Chicken cytochrome BC1 complex with ZN++ and an iodinated derivat... -

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Basic information

Entry
Database: PDB / ID: 3h1k
TitleChicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound
Components
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ...) x 4
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ...) x 2
  • Cytochrome b
  • MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
KeywordsOXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / UBIQUINONE / REDOX ENZYME / ZINC / KRESOXIM-METHYL / RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE IRON / MEMBRANE / METAL-BINDING / MITOCHONDRION / TRANSMEMBRANE / Iron / Mitochondrion inner membrane / Transport / Disulfide bond / Iron-sulfur / Transit peptide
Function / homology
Function and homology information


Respiratory electron transport / Complex III assembly / quinol-cytochrome-c reductase / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress ...Respiratory electron transport / Complex III assembly / quinol-cytochrome-c reductase / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / metal ion binding / membrane / cytoplasm
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C ...Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-IKR / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Cytochrome c / Complex III subunit 9 ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-IKR / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Cytochrome c / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 / Cytochrome b-c1 complex subunit 7 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i / Cytochrome b-c1 complex subunit 8 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 3.48 Å
AuthorsBerry, E.A. / Zhang, Z. / Bellamy, H.D. / Huang, L.S.
CitationJournal: Biochim.Biophys.Acta / Year: 2000
Title: Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex
Authors: Berry, E.A. / Zhang, Z. / Bellamy, H.D. / Huang, L.
History
DepositionApr 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 6, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
B: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
C: Cytochrome b
D: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
G: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
H: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
N: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
O: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
P: Cytochrome b
Q: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
R: Cytochrome b-c1 complex subunit Rieske, mitochondrial
S: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
T: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
U: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
V: Cytochrome b-c1 complex subunit Rieske, mitochondrial
W: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,85056
Polymers462,06520
Non-polymers18,78536
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area102300 Å2
ΔGint-764 kcal/mol
Surface area159470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.717, 181.297, 241.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO

#1: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I


Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX31*PLUS, quinol-cytochrome-c reductase
#2: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX29*PLUS, quinol-cytochrome-c reductase

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Protein , 2 types, 4 molecules CPDQ

#3: Protein Cytochrome b / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit / Cytochrome b-c1 complex subunit 3 / ...Ubiquinol-cytochrome-c reductase complex cytochrome b subunit / Cytochrome b-c1 complex subunit 3 / Complex III subunit 3 / Complex III subunit III


Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946, quinol-cytochrome-c reductase
#4: Protein MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN


Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX26*PLUS, quinol-cytochrome-c reductase

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Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules ERIV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex ...Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex III subunit 5


Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: sequence database residues 77-272 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex ...Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex III subunit 5


Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-76 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase

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MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 4 types, 8 molecules FSGTHUJW

#6: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN


Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX30*PLUS, quinol-cytochrome-c reductase
#7: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C


Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX32*PLUS, quinol-cytochrome-c reductase
#8: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX28*PLUS, quinol-cytochrome-c reductase
#10: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN


Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX27*PLUS, quinol-cytochrome-c reductase

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Sugars , 1 types, 5 molecules

#20: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 11 types, 48 molecules

#11: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#12: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#13: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#14: Chemical ChemComp-IKR / methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate


Mass: 453.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20INO4
#15: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#16: 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
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#19: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#21: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ...IN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ALIGNMENT IS UNKNOWN FOR THE FIRST 40 RESIDUES IN CHAINS I AND V.

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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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000. The Kresoxim-methyl derivative WAS ADDED to the protein FROM ETHANOLIC SOLUTION. After verifying good diffraction by these ...Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000. The Kresoxim-methyl derivative WAS ADDED to the protein FROM ETHANOLIC SOLUTION. After verifying good diffraction by these crystals, some were transferred to a drop of mother liquor supplemented with glycerol and ~0.2 mM ZnCl2. After 1 week this crystal was flash-cooled for data collection. During analysis of Zn binding presence of the inhibitor was overlooked, and in the primary citation publication the anomalous signal of I in the inhibitor was mistakenly attributed to a second Zn binding site, Zn02. VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.283 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 3.48→42.61 Å / Num. all: 87072 / Num. obs: 87072 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 84.8 Å2 / Rsym value: 0.204 / Net I/σ(I): 9.49
Reflection shellResolution: 3.48→3.55 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.14 / Num. unique all: 3144 / Rsym value: 0.99 / % possible all: 65.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1BCC after further correction/refinement

1bcc


Resolution: 3.48→18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4943137.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2558 3 %RANDOM
Rwork0.239 ---
all0.24 86369 --
obs0.24 86369 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8112 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 110.4 Å2
Baniso -1Baniso -2Baniso -3
1-42.14 Å20 Å20 Å2
2---32.46 Å20 Å2
3----9.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.48→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31820 0 836 17 32673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.532.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.48→3.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.384 317 3 %
Rwork0.334 10242 -
obs-10559 77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2hetero10.par&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ikr.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5prosthw.par&_1_TOPOLOGY_INFILE_5

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