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- PDB-4hcg: Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with ... -

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Basic information

Entry
Database: PDB / ID: 4hcg
TitleUncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with Zinc bound from Bacillus anthracis
ComponentsCupredoxin 1
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / beta-fold / beta sandwich / Greek-key beta-barrel
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 (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.847 Å
AuthorsKim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with Zinc bound from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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 / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _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: Cupredoxin 1
B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5047
Polymers22,1772
Non-polymers3275
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-87 kcal/mol
Surface area10220 Å2
MethodPISA
2
A: Cupredoxin 1
hetero molecules

B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5047
Polymers22,1772
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+3/41
Buried area980 Å2
ΔGint-79 kcal/mol
Surface area10300 Å2
MethodPISA
3
A: Cupredoxin 1
hetero molecules

B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5047
Polymers22,1772
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Buried area1580 Å2
ΔGint-53 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 52.500, 172.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cupredoxin 1


Mass: 11088.687 Da / Num. of mol.: 2 / Fragment: UNP residues 33-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_1561, GBAA_1561 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20 % w/v PEG 8000, 10 mM zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 21650 / Num. obs: 21650 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 26.96 Å2 / Rsym value: 0.103 / Net I/σ(I): 7.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.84 / Num. unique all: 1074 / Rsym value: 0.828 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: dev_1032)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.847→36.288 Å / SU ML: 0.14 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.91 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1103 5.14 %random
Rwork0.165 ---
all0.167 21477 --
obs0.167 21477 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2 Å2
Refinement stepCycle: LAST / Resolution: 1.847→36.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 5 154 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071530
X-RAY DIFFRACTIONf_angle_d1.1182073
X-RAY DIFFRACTIONf_dihedral_angle_d13.209597
X-RAY DIFFRACTIONf_chiral_restr0.076248
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8475-1.93150.2181500.18882453260399
1.9315-2.03340.19221260.17352474260099
2.0334-2.16070.22831390.171824882627100
2.1607-2.32760.19171330.16522511264499
2.3276-2.56170.22171500.171125152665100
2.5617-2.93230.19371310.178525622693100
2.9323-3.69380.19491360.164225932729100
3.6938-36.29460.16831380.154527782916100
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)
11.6131-0.4362-0.80591.7611-0.83892.80150.25580.28650.1233-0.2229-0.1417-0.2593-0.27570.6197-0.07240.2752-0.00030.02920.32460.06320.337418.032522.150745.6143
24.06-0.64910.66681.7896-0.23884.55730.16360.20820.0507-0.1495-0.2662-0.31980.1290.50730.05120.13640.02880.03470.21810.07740.221318.639614.589948.0618
32.1199-1.1247-0.6391.191-0.41891.76510.06420.21560.0067-0.0442-0.02560.0382-0.2542-0.154-0.02290.15880.0162-0.00120.22480.03210.19328.629615.783450.5594
42.05431.4306-0.78412.811-3.19354.3930.3161-0.12840.26640.011-0.26430.5230.26670.053-0.10780.2842-0.0683-0.04210.24780.02260.208116.8061-5.880178.1814
53.3541-0.08631.05042.0633-0.37492.05350.03840.0549-0.1676-0.07810.03940.06210.2855-0.2081-0.0310.2284-0.0343-0.00460.21320.02880.179520.6551-1.208972.0153
62.19850.77620.3853.0329-1.39762.5773-0.04540.1861-0.162-0.33180.1032-0.09570.4095-0.0646-0.0610.2694-0.0199-0.02040.219-0.02620.182821.6737-1.398467.2029
71.92660.3878-0.34062.44830.64221.7093-0.0464-0.0338-0.1671-0.17040.11390.05120.3154-0.0511-0.06660.2275-0.0203-0.0230.21960.05430.240529.806-1.836874.6172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 128 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 49 )
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 128 )

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