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- PDB-1ztd: Hypothetical Protein Pfu-631545-001 From Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 1ztd
TitleHypothetical Protein Pfu-631545-001 From Pyrococcus furiosus
ComponentsHypothetical Protein Pfu-631545-001Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PROTEIN STRUCTURE INITIATIVE / PSI / CONSERVED HYPOTHETICAL PROTEIN / PYROCOCCUS FURIOSUS / HYPERTHERMOPHILE / Pfu-631545-001
Function / homology
Function and homology information


ribonuclease III activity / RNA processing
Similarity search - Function
Ribonuclease III / Ribonuclease III, archaeal / Ribonuclease III superfamily, archaeal / Ribonuclease III / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III, endonuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFu, Z.-Q. / Horanyi, P. / Florence, Q. / Liu, Z.-J. / Chen, L. / Lee, D. / Habel, J. / Xu, H. / Nguyen, D. / Chang, S.-H. ...Fu, Z.-Q. / Horanyi, P. / Florence, Q. / Liu, Z.-J. / Chen, L. / Lee, D. / Habel, J. / Xu, H. / Nguyen, D. / Chang, S.-H. / Zhou, W. / Zhang, H. / Jenney Jr., F.E. / Sha, B. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Hypothetical Protein Pfu-631545-001 From Pyrococcus furiosus
Authors: Fu, Z.-Q. / Horanyi, P. / Florence, Q. / Liu, Z.-J. / Chen, L. / Lee, D. / Habel, J. / Xu, H. / Nguyen, D. / Chang, S.-H. / Zhou, W. / Zhang, H. / Jenney Jr., F.E. / Sha, B. / Adams, M.W.W. ...Authors: Fu, Z.-Q. / Horanyi, P. / Florence, Q. / Liu, Z.-J. / Chen, L. / Lee, D. / Habel, J. / Xu, H. / Nguyen, D. / Chang, S.-H. / Zhou, W. / Zhang, H. / Jenney Jr., F.E. / Sha, B. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE Currently there is no protein sequence database reference available for this entry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical Protein Pfu-631545-001
B: Hypothetical Protein Pfu-631545-001


Theoretical massNumber of molelcules
Total (without water)29,4702
Polymers29,4702
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.352, 61.093, 51.582
Angle α, β, γ (deg.)90.00, 97.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical Protein Pfu-631545-001 / Hypothesis


Mass: 14735.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET24D BAM / Production host: Escherichia coli (E. coli) / Strain (production host): C41 PRIL / References: UniProt: Q8U363
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.06 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291 K / pH: 8.2
Details: 5% w/v PEG-8000, pH 8.2, Sitting Drop, Vapor Diffusion, temperature 291K, pH 8.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97941
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2→35.97 Å / Num. obs: 15035 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 9.92 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.0825 / Rsym value: 0.0825 / Net I/σ(I): 18.72
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5.07 / Rsym value: 0.229 / % possible all: 86.3

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
LSCALEdata scaling
SGXPROphasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 260232.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.272 758 5 %RANDOM
Rwork0.234 ---
obs0.234 15008 98.5 %-
all-15008 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.89 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 25.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2---4.8 Å20 Å2
3---3.551 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.04 Å
Refinement stepCycle: LAST / Resolution: 2→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 0 63 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 69 5.3 %
Rwork0.237 1239 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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