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- PDB-1zd0: Crystal structure of Pfu-542154 conserved hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1zd0
TitleCrystal structure of Pfu-542154 conserved hypothetical protein
Componentshypothetical protein PF0523
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


PF0523-like / CGI121/TPRKB / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHANOL / : / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / SAD / Resolution: 1.7 Å
AuthorsHabel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. ...Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structure of Pfu-542154 conserved hypothetical protein
Authors: Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. ...Authors: Habel, J.E. / Liu, Z.J. / Horanyi, P.S. / Florence, Q.J.T. / Tempel, W. / Zhou, W. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.H. / Bereton, P. / Izumi, M. / Jenny Jr., F.E. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Rose, J.P. / Wang, B.C.
History
DepositionApr 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PF0523
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,97218
Polymers16,8521
Non-polymers12017
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.460, 53.460, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein hypothetical protein PF0523


Mass: 16851.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0523 / Plasmid: pET24 DBAM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 18976895, UniProt: Q8U3E5*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#4: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.140.8
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931modified microbatch7.7Magnesium Acetate and PEG 3350, pH 7.7, modified microbatch, temperature 293K
2932modified microbatch7.7Magnesium Acetate, Methanol, and PEG 3350, pH 7.7, modified microbatch, temperature 293K
2933modified microbatch7.7Magnesium Acetate, Methanol, and PEG 3350, pH 7.7, modified microbatch, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97
ROTATING ANODERIGAKU MICROMAX-00722.29
ROTATING ANODERIGAKU FR-D32.29
Detector
TypeIDDetectorDate
MARRESEARCH1CCDDec 17, 2004
RIGAKU RAXIS IV2IMAGE PLATEJan 5, 2005
RIGAKU RAXIS IV3IMAGE PLATEMar 4, 2005
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
3SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
22.291
ReflectionResolution: 1.7→50 Å / Num. obs: 15870 / % possible obs: 98.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.045 / Χ2: 1.235
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.764.30.2113441.16185.1
1.76-1.836.80.19115311.0296.6
1.83-1.919.40.14115991.07499.9
1.91-2.0210.60.10115881.074100
2.02-2.1410.80.07716131.183100
2.14-2.3110.80.0615731.21899.9
2.31-2.5410.80.05116181.252100
2.54-2.9110.70.04616161.411100
2.91-3.6610.60.0416431.533100
3.66-509.80.03617451.24999.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM : 0.3 / Reflection: 5262
Phasing MAD shell
Resolution (Å)FOM Reflection
8.52-200.28297
5.54-8.520.33456
4.38-5.540.35575
3.74-4.380.32642
3.31-3.740.29727
3-3.310.32800
2.77-30.3855
2.58-2.770.26910
Phasing dmFOM : 0.54 / FOM acentric: 0.56 / FOM centric: 0.46 / Reflection: 5906 / Reflection acentric: 4908 / Reflection centric: 998
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-19.6580.880.880.76282169113
4.3-6.90.80.840.67828631197
3.4-4.30.750.790.611000812188
3-3.40.610.650.39985829156
2.6-30.430.460.2417431517226
2.4-2.60.180.190.111068950118

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0005refinement
RefinementMethod to determine structure: SAS / Resolution: 1.7→46.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.79 / SU ML: 0.086 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: Engh & Huber
Details: ARP/WARP and MOLPROBITY were also used in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.252 797 5 %RANDOM
Rwork0.202 ---
all0.205 ---
obs-15838 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 20 93 1187
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01611560.022
X-RAY DIFFRACTIONr_angle_refined_deg1.42215571.966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.241405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.9295226.154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4523415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.471415
X-RAY DIFFRACTIONr_chiral_restr0.11920.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0068150.02
X-RAY DIFFRACTIONr_nbd_refined0.2335870.2
X-RAY DIFFRACTIONr_nbtor_refined0.3048210.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.151880.2
X-RAY DIFFRACTIONr_metal_ion_refined0.02710.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.276620.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.114150.2
X-RAY DIFFRACTIONr_mcbond_it0.9817381.5
X-RAY DIFFRACTIONr_mcangle_it1.4711602
X-RAY DIFFRACTIONr_scbond_it2.1294703
X-RAY DIFFRACTIONr_scangle_it3.013974.5
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 50 -
Rwork0.29 918 -
obs--82.88 %

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