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- PDB-2hjm: Crystal structure of a singleton protein PF1176 from P. furiosus -

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Basic information

Entry
Database: PDB / ID: 2hjm
TitleCrystal structure of a singleton protein PF1176 from P. furiosus
ComponentsHypothetical protein PF1176
Keywordsstructural genomics / unknown function / Singleton protein pf1176 / SECSG / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics
Function / homologyprotein pf1176 like / Domain of unknown function, DUF3216 / Pf1176-like superfamily / Protein of unknown function (DUF3216) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DUF3216 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsChen, L.Q. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structure of a singleton protein PF1176 from P. furiosus
Authors: Rose, J.P. / Liu, Z.-J. / Wang, B.-C.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PF1176
B: Hypothetical protein PF1176
C: Hypothetical protein PF1176
D: Hypothetical protein PF1176


Theoretical massNumber of molelcules
Total (without water)48,1744
Polymers48,1744
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Hypothetical protein PF1176
D: Hypothetical protein PF1176


Theoretical massNumber of molelcules
Total (without water)24,0872
Polymers24,0872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area8780 Å2
MethodPISA
3
A: Hypothetical protein PF1176
B: Hypothetical protein PF1176


Theoretical massNumber of molelcules
Total (without water)24,0872
Polymers24,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-18 kcal/mol
Surface area9110 Å2
MethodPISA
4
A: Hypothetical protein PF1176
C: Hypothetical protein PF1176


Theoretical massNumber of molelcules
Total (without water)24,0872
Polymers24,0872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area9170 Å2
MethodPISA
5
B: Hypothetical protein PF1176

D: Hypothetical protein PF1176


Theoretical massNumber of molelcules
Total (without water)24,0872
Polymers24,0872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
Buried area1800 Å2
ΔGint-9 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.680, 64.240, 111.650
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
Hypothetical protein PF1176


Mass: 12043.573 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pf1176 / Plasmid: pf1176 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 100mM Na3 Citrate pH 5.2, 30% PEG400, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2006 / Details: Rosenbaum
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 12787 / Num. obs: 12787 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 3.53 / Num. unique all: 1242 / Rsym value: 0.6 / % possible all: 98.9

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Processing

Software
NameClassification
SCA2STRUCTUREmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1437 -Random
Rwork0.2276 ---
all0.23 19286 --
obs0.23 18779 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 0 2 2587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.16

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