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- PDB-1u0k: The structure of a Predicted Epimerase PA4716 from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 1u0k
TitleThe structure of a Predicted Epimerase PA4716 from Pseudomonas aeruginosa
Componentsgene product PA4716
Keywordsstructural genomics / unknown function / sctructural genomics / MCSG / Pseudomonas aeruginosa / protein structure initiative / PSI / Midwest Center for Structural Genomics
Function / homologyPhenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / isomerase activity / Roll / cytoplasm / Alpha Beta / PhzF family phenazine biosynthesis protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsCuff, M.E. / Ginell, S.L. / Rotella, F.J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of hypothetical protein PA4716 from Pseudomonas aeruginosa
Authors: Cuff, M.E. / Ginell, S.J. / Rotella, F.J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 14, 2019Group: Data collection / Derived calculations / Structure summary
Category: audit_author / struct_conn
Item: _audit_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gene product PA4716
B: gene product PA4716


Theoretical massNumber of molelcules
Total (without water)62,7292
Polymers62,7292
Non-polymers00
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-8 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.778, 69.477, 94.950
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein gene product PA4716


Mass: 31364.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4716 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: di-Ammonium Citrate, PEG 3350, sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97959 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 19, 2004 / Details: SBC2
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 75759 / Num. obs: 75759 / % possible obs: 98.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5.74 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→91.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.273 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18867 4008 5 %RANDOM
Rwork0.16718 ---
all0.16827 77163 --
obs0.16827 75759 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.17 Å2
2---0.65 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 0 913 5262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214455
X-RAY DIFFRACTIONr_bond_other_d0.0020.024077
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9516055
X-RAY DIFFRACTIONr_angle_other_deg0.76139364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645564
X-RAY DIFFRACTIONr_chiral_restr0.0780.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025122
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021000
X-RAY DIFFRACTIONr_nbd_refined0.2070.2947
X-RAY DIFFRACTIONr_nbd_other0.2460.24975
X-RAY DIFFRACTIONr_nbtor_other0.0780.22797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2721
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.2123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.282
X-RAY DIFFRACTIONr_mcbond_it0.7171.52805
X-RAY DIFFRACTIONr_mcangle_it1.37524433
X-RAY DIFFRACTIONr_scbond_it2.02231650
X-RAY DIFFRACTIONr_scangle_it3.3834.51622
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 288
Rwork0.214 5573

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