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- PDB-5tk2: Crystal Structure of Uncharacterized Cupredoxin-like domain prote... -

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Basic information

Entry
Database: PDB / ID: 5tk2
TitleCrystal Structure of Uncharacterized Cupredoxin-like domain protein from Bacillus anthracis
ComponentsCytochrome B
KeywordsOXIDOREDUCTASE / Cupredoxin / 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
: / FORMIC ACID / D-MALATE / 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: 1.4 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 1.1Dec 14, 2016Group: Database references / Structure summary
Revision 1.2Feb 8, 2017Group: Database references / Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.6Nov 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
C: Cytochrome B
D: Cytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,31513
Polymers44,3554
Non-polymers9609
Water7,422412
1
A: Cytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3353
Polymers11,0891
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3974
Polymers11,0891
Non-polymers3093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2012
Polymers11,0891
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3814
Polymers11,0891
Non-polymers2933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.226, 58.023, 108.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-379-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome B / Uncharacterized protein


Mass: 11088.687 Da / Num. of mol.: 4 / 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 gold / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS

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Non-polymers , 5 types, 421 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30.9 % w/v PEG4000, 150 mM Malate pH 5.0, 60 mM Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.507
11h,-k,-l20.493
ReflectionResolution: 1.4→50 Å / Num. obs: 75414 / % possible obs: 94.7 % / Redundancy: 2.9 % / Rsym value: 0.065 / Net I/σ(I): 25.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.6 / % possible all: 61.1

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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: 1.4→24.25 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.187 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16595 3778 5 %RANDOM
Rwork0.1346 ---
obs0.13618 71571 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.411 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20.14 Å2
2---3.46 Å2-0 Å2
3---1.85 Å2
Refinement stepCycle: 1 / Resolution: 1.4→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 38 412 3213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192900
X-RAY DIFFRACTIONr_bond_other_d0.0010.022977
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.0053908
X-RAY DIFFRACTIONr_angle_other_deg0.68536919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97326.19105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80615597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.532156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
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_restr4.48432900
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded12.00752866
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 193 -
Rwork0.228 3374 -
obs--60.79 %

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