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- PDB-2guk: Crystal Structure of the Conserved Protein of Unknown Function fr... -

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Basic information

Entry
Database: PDB / ID: 2guk
TitleCrystal Structure of the Conserved Protein of Unknown Function from Porphyromonas gingivalis
Componentshypothetical protein PG1857Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / alpha-helical bundle / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPG1857-like / PG1857-like / Domain of unknown function DUF2023 / PG1857-like superfamily / Protein of unknown function (DUF2023) / 2-Layer Sandwich / Alpha Beta / : / DUF2023 domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsKim, Y. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Conserved Hypothetical Protein from Porphyromonas gingivalis
Authors: Kim, Y. / Quartey, P. / Moy, S. / Joachimiak, A.
History
DepositionMay 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Remark 300THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO EXPERIMENTAL EVIDENCE ABOUT THE BIOLOGICAL UNIT. THE BIOLOGICAL UNIT COULD BE A DIMER (AS IN THE ASYMMETRIC UNIT) OR A TETRAMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PG1857
B: hypothetical protein PG1857


Theoretical massNumber of molelcules
Total (without water)28,3872
Polymers28,3872
Non-polymers00
Water2,378132
1
A: hypothetical protein PG1857
B: hypothetical protein PG1857

A: hypothetical protein PG1857
B: hypothetical protein PG1857


Theoretical massNumber of molelcules
Total (without water)56,7734
Polymers56,7734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)50.028, 50.028, 186.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein hypothetical protein PG1857 / Hypothesis


Mass: 14193.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG1587, GeneID:2551814 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 34541468, UniProt: Q7MTT4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 40.27 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% iso-propanol, 0.1 M HEPES 7.5, 10 % PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 275K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.91→34.76 Å / Num. all: 20138 / Num. obs: 19279 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.5
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1825 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→34.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.435 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28056 1953 10.2 %RANDOM
Rwork0.23253 ---
all0.23742 17168 --
obs0.23742 17168 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 132 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9642652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09322.264106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831527
X-RAY DIFFRACTIONr_chiral_restr0.1270.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021541
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21004
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9571.51199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48421902
X-RAY DIFFRACTIONr_scbond_it2.2193840
X-RAY DIFFRACTIONr_scangle_it3.3324.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.394 137
Rwork0.309 1192
obs-1192
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.20190.8366-1.36840.61910.0121.78980.02690.10720.21080.01150.04160.09840.00530.0815-0.06850.0362-0.0464-0.04630.01650.0819-0.069731.97228.361110.458
20.42580.3546-1.06960.3164-1.0914.596-0.0224-0.0013-0.0625-0.04720.06560.03920.32660.2014-0.04320.03390.00240.02560.06180.0116-0.033548.32326.26186.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1147 - 117
2X-RAY DIFFRACTION2BB6 - 1179 - 120

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