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- PDB-3cyg: Crystal structure of an uncharacterized protein from Fervidobacte... -

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Basic information

Entry
Database: PDB / ID: 3cyg
TitleCrystal structure of an uncharacterized protein from Fervidobacterium nodosum Rt17-B1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized Protein / PSI-II / 10495j / Fervibacterium nodosum / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex ...Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DUF3298/DUF4163 domain-containing protein
Similarity search - Component
Biological speciesFervidobacterium nodosum Rt17-B1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from Fervidobacterium nodosum Rt17-B1.
Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,9612
Polymers52,9612
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,4801
Polymers26,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,4801
Polymers26,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.228, 72.794, 166.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 26480.303 Da / Num. of mol.: 2 / Fragment: Residues 37-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium nodosum Rt17-B1 (bacteria)
Species: Fervidobacterium nodosum / Strain: Rt17-B1 / DSM 5306 / Gene: Fnod_1146 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(RIPL) / References: UniProt: A7HM60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3500, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 15697 / Num. obs: 15697 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 68.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 2.61→2.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1 / Num. unique all: 883 / % possible all: 54.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.61→36.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 69967.1 / 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
Rfree0.299 746 5 %RANDOM
Rwork0.244 ---
all0.29 15697 --
obs0.244 14982 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.1183 Å2 / ksol: 0.29191 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.55 Å20 Å20 Å2
2--5.58 Å20 Å2
3----15.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.61→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 69 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.61→2.76 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 66 4.1 %
Rwork0.34 1561 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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