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- PDB-2apl: Crystal structure of protein PG0816 from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 2apl
TitleCrystal structure of protein PG0816 from Porphyromonas gingivalis
Componentshypothetical protein PG0816
KeywordsStructural genomics / unknown function / Porphyromonas gingivalis / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPG0816-like / PG0816-like / Protein of unknown function DUF1896 / PG0816-like superfamily / Domain of unknown function (DUF1896) / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / DUF1896 domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsChang, C. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein PG0816 from Porphyromonas gingivalis
Authors: Chang, C. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionAug 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PG0816


Theoretical massNumber of molelcules
Total (without water)17,8851
Polymers17,8851
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.947, 55.159, 80.984
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 PG0816


Mass: 17885.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Plasmid details: pMCSG / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MW33
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Acetate, Bis-Tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12416 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 52.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 11.2 / % possible all: 71.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→45.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.426 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23367 605 4.9 %RANDOM
Rwork0.19692 ---
all0.1987 12374 --
obs0.1987 12374 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.682 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---0.92 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.01→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 0 80 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9761660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88724.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.696155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02937
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2573
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2855
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.5773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71521212
X-RAY DIFFRACTIONr_scbond_it3.1213502
X-RAY DIFFRACTIONr_scangle_it4.6094.5448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 41 -
Rwork0.213 683 -
obs--77.93 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07650.26011.43320.67630.16385.2364-0.0105-0.019-0.241-0.20090.20920.06290.107-0.1158-0.19870.0722-0.053-0.002-0.1782-0.0208-0.130936.14847.8641.224
20.71290.3120.27054.5919-2.65237.2494-0.0010.05090.10990.22420.46960.4378-0.3214-0.5044-0.4685-0.06220.02440.0402-0.15850.0825-0.120536.59737.12327.232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 703 - 70
2X-RAY DIFFRACTION2AA71 - 15071 - 150

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