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- PDB-5tk4: Crystal Structure of Uncharacterized Cupredoxin-like Domain Prote... -

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Basic information

Entry
Database: PDB / ID: 5tk4
TitleCrystal Structure of Uncharacterized Cupredoxin-like Domain Protein from Bacillus anthracis
ComponentsCytochrome B
KeywordsOXIDOREDUCTASE / ICupredoxin fold / beta-sandwich / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


EfeO-type cupredoxin-like domain / Cupredoxin-like domain / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
EfeO-type cupredoxin-like domain-containing protein / EfeO-type cupredoxin-like domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsKim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Uncharacterized Cupredoxin-like Domain Protein from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome B
B: Cytochrome B


Theoretical massNumber of molelcules
Total (without water)22,2732
Polymers22,2732
Non-polymers00
Water4,828268
1
A: Cytochrome B


Theoretical massNumber of molelcules
Total (without water)11,1371
Polymers11,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome B


Theoretical massNumber of molelcules
Total (without water)11,1371
Polymers11,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.695, 42.695, 100.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cytochrome B / Uncharacterized protein


Mass: 11136.685 Da / Num. of mol.: 2 / Fragment: UNP residues 33-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 34.3 % w/v PEG 4000, 150 mM Formate pH 4.0, 7 mM Nickel Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11-H, K, -L20.49
ReflectionResolution: 1.46→50 Å / Num. obs: 31013 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rsym value: 0.085 / Net I/σ(I): 26.9
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.839 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCI

4hci


Resolution: 1.46→26.33 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.135 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.013 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16276 1551 5 %RANDOM
Rwork0.12782 ---
obs0.12948 29402 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.46→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 268 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191542
X-RAY DIFFRACTIONr_bond_other_d0.0010.021578
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.0012093
X-RAY DIFFRACTIONr_angle_other_deg0.70133672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5926.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415.032314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.734152
X-RAY DIFFRACTIONr_chiral_restr0.0780.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.1631542
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded7.83651515
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 98 -
Rwork0.124 2082 -
obs--94.58 %

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