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- PDB-1xe1: Hypothetical Protein From Pyrococcus Furiosus Pfu-880080-001 -

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Basic information

Entry
Database: PDB / ID: 1xe1
TitleHypothetical Protein From Pyrococcus Furiosus Pfu-880080-001
Componentshypothetical protein PF0907
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein structure initiative / SECSG / Pyrococcus furiosus / Conserved hypothetical protein / hyperthermophile / PSI / Southeast Collaboratory for Structural Genomics
Function / homologyUncharacterised conserved protein UCP019072 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / Beta Barrel / Mainly Beta / Elongation factor Tu-type domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, J.C. / Zhao, M. / Zhou, W. / Liu, Z.J. / Tempel, W. / Arendall III, W.B. / Chen, L. / Lee, D. / Habel, J.E. / Rose, J.P. ...Chang, J.C. / Zhao, M. / Zhou, W. / Liu, Z.J. / Tempel, W. / Arendall III, W.B. / Chen, L. / Lee, D. / Habel, J.E. / Rose, J.P. / Richardson, J.S. / Richardson, D.C. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Hypothetical Protein From Pyrococcus Furiosus Pfu-880080-001
Authors: Chang, J.C. / Zhao, M. / Zhou, W. / Liu, Z.J. / Tempel, W. / Arendall III, W.B. / Chen, L. / Lee, D. / Habel, J.E. / Rose, J.P. / Richardson, J.S. / Richardson, D.C. / Wang, B.C. / Southeast ...Authors: Chang, J.C. / Zhao, M. / Zhou, W. / Liu, Z.J. / Tempel, W. / Arendall III, W.B. / Chen, L. / Lee, D. / Habel, J.E. / Rose, J.P. / Richardson, J.S. / Richardson, D.C. / Wang, B.C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. 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 PF0907
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8942
Polymers12,7981
Non-polymers961
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: hypothetical protein PF0907
hetero molecules

A: hypothetical protein PF0907
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7874
Polymers25,5952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1200 Å2
ΔGint-36 kcal/mol
Surface area9570 Å2
MethodPISA
3
A: hypothetical protein PF0907
hetero molecules

A: hypothetical protein PF0907
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7874
Polymers25,5952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area1170 Å2
ΔGint-25 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.625, 88.625, 73.267
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein hypothetical protein PF0907


Mass: 12797.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2D2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: modified microbatch / pH: 6.5
Details: 1.6M magnesium sulfate, 0.1M MES, pH 6.5, modified microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2004
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11239 / % possible obs: 93.7 % / Rmerge(I) obs: 0.068 / Χ2: 1.049
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
2-2.070.4436651.232157.4
2.07-2.150.4789701.423182.6
2.15-2.250.32311181.151196.1
2.25-2.370.25411680.865199.7
2.37-2.520.21811810.8051100
2.52-2.710.1611850.8011100
2.71-2.990.09711890.8811100
2.99-3.420.06812121.2161100
3.42-4.310.06512241.3221100
4.31-500.04613271.2199.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.4 Å / D res low: 20 Å / FOM : 0.35 / Reflection: 2567
Phasing MAD shell
Resolution (Å)FOM Reflection
10.92-200.21162
7.35-10.920.31235
5.88-7.350.36280
5.04-5.880.35315
4.48-5.040.37348
4.07-4.480.38387
3.76-4.070.36407
3.51-3.760.36433
Phasing dmFOM : 0.49 / FOM acentric: 0.48 / FOM centric: 0.52 / Reflection: 6675 / Reflection acentric: 5367 / Reflection centric: 1308
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-19.3060.930.930.78335181154
4.3-6.90.850.90.71982706276
3.4-4.30.810.840.671180925255
3-3.40.550.560.521167965202
2.6-30.230.230.2419301643287
2.4-2.60.080.080.091081947134

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Processing

Software
NameVersionClassificationNB
SOLVE2.03phasing
RESOLVE2.03phasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1data extraction
MAR345data collection
REFMAC5refinement
RefinementMethod to determine structure: SAD / Resolution: 2→76.696 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.221 / ESU R: 0.135 / ESU R Free: 0.126
RfactorNum. reflection% reflection
Rfree0.2397 525 4.682 %
Rwork0.2213 --
obs0.22219 11213 93.582 %
Solvent computationSolvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 41.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.078 Å20.039 Å20 Å2
2--0.078 Å20 Å2
3----0.117 Å2
Refinement stepCycle: LAST / Resolution: 2→76.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 5 28 685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022664
X-RAY DIFFRACTIONr_angle_refined_deg1.4652.001891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.124590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92225.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6815127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.522153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02465
X-RAY DIFFRACTIONr_nbd_refined0.20.2237
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0160.21
X-RAY DIFFRACTIONr_mcbond_it2.52442
X-RAY DIFFRACTIONr_mcangle_it4.0223710
X-RAY DIFFRACTIONr_scbond_it3.3562222
X-RAY DIFFRACTIONr_scangle_it5.3943181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0510.5190.33342585951.688
2.051-2.1070.302280.31859984474.289
2.107-2.1680.261330.27169281888.631
2.168-2.2350.277400.24772679796.11
2.235-2.3080.262320.24172976699.347
2.308-2.3890.23360.248716752100
2.389-2.4790.224350.245690725100
2.479-2.580.267410.229653694100
2.58-2.6950.294310.257650681100
2.695-2.8260.33400.248610650100
2.826-2.9790.171200.252594614100
2.979-3.1590.254290.225553582100
3.159-3.3770.331330.222525558100
3.377-3.6470.254260.198491517100
3.647-3.9940.211220.19462484100
3.994-4.4640.195180.166429447100
4.464-5.1510.202150.167379394100
5.151-6.3020.11770.228339346100
6.302-8.8820.161120.232266278100
8.882-76.6960.19180.28716017695.455

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