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- PDB-3cvg: Crystal structure of a periplasmic putative metal binding protein -

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Basic information

Entry
Database: PDB / ID: 3cvg
TitleCrystal structure of a periplasmic putative metal binding protein
ComponentsPutative metal binding protein
KeywordsMETAL BINDING PROTEIN / PSI-II / NYSGXRC / periplasmic / metal binding / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyProtein of unknown function DUF3435 / Protein of unknown function (DUF3435) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / C2H2-type domain-containing protein / :
Function and homology information
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a periplasmic putative metal binding protein.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metal binding protein
B: Putative metal binding protein
C: Putative metal binding protein
D: Putative metal binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7098
Polymers131,5484
Non-polymers1604
Water9,368520
1
A: Putative metal binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,8871
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative metal binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,8871
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative metal binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,8871
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative metal binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,8871
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-39.3 kcal/mol
Surface area42360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.782, 150.782, 116.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-529-

HOH

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Components

#1: Protein
Putative metal binding protein


Mass: 32887.109 Da / Num. of mol.: 4 / Fragment: Residues 22-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_05057 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(RIPL) / References: UniProt: Q1DXA6, UniProt: J3KFC8*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Bis-tris, PEG 3350, MgCl2, CaCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 103728 / Num. obs: 103728 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 22.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1 / Num. unique all: 8575 / % possible all: 82.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→44.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 80706.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2721 3 %RANDOM
Rwork0.259 ---
obs0.259 89743 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3325 Å2 / ksol: 0.331079 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20 Å2
2--1.77 Å20 Å2
3----3.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.97→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7962 0 4 520 8486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 429 3.1 %
Rwork0.293 13290 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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