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- PDB-2a35: 1.5 A Crystal Structure of a Protein of Unknown Function PA4017 f... -

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Basic information

Entry
Database: PDB / ID: 2a35
Title1.5 A Crystal Structure of a Protein of Unknown Function PA4017 from Pseudomonas aeruginosa PAO1, Possible Epimerase
Componentshypothetical protein PA4017
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pseudomonas aeruginosa / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein Him1/Fmp52 / HIM1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Oxidoreductase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Xu, L. / Cuff, M. / Savchenko, A. / Cymborowski, M. / Minor, W. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a hypothetical protein PA4017 from Pseudomonas aeruginosa PAO1
Authors: Zhang, R. / Xu, L. / Cuff, M. / Savchenko, A. / Cymborowski, M. / Minor, W. / Edwards, A. / Joachimiak, A.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 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 1.3Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PA4017
B: hypothetical protein PA4017


Theoretical massNumber of molelcules
Total (without water)46,6802
Polymers46,6802
Non-polymers00
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-6 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.762, 98.762, 71.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThis protein existed as dimer. The deposited coords. of MolA and MolB form the biological dimer.

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Components

#1: Protein hypothetical protein PA4017


Mass: 23339.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: gi:9950210 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HX10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 34% PEGMME, pH 8.5, 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: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 63433 / Num. obs: 63370 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 46.67
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6279 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→85.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.527 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20395 3211 5.1 %RANDOM
Rwork0.17423 ---
all0.1757 63433 --
obs0.17573 60114 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.5→85.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 537 3691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223212
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9994349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.885412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48722.977131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4071530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022412
X-RAY DIFFRACTIONr_nbd_refined0.2030.21636
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2459
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.266
X-RAY DIFFRACTIONr_mcbond_it0.8261.52125
X-RAY DIFFRACTIONr_mcangle_it1.35123275
X-RAY DIFFRACTIONr_scbond_it2.19831207
X-RAY DIFFRACTIONr_scangle_it3.4814.51074
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 247 -
Rwork0.21 4405 -
obs--100 %
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)
10.10880.0040.09640.68940.23490.4523-0.0289-0.0153-0.0213-0.03950.020.0589-0.0380.02570.0089-0.0046-0.0022-0.006-0.02540.0057-0.008114.565975.03735.5463
20.371-0.1074-0.28140.3256-0.00860.806-0.01340.01740.00420.0042-0.01480.0280.00970.00610.0282-0.02170.0116-0.0028-0.014-0.001-0.011816.908368.883637.6253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 904 - 90
2X-RAY DIFFRACTION1AA91 - 17091 - 170
3X-RAY DIFFRACTION1AA175 - 215175 - 215
4X-RAY DIFFRACTION2BB4 - 904 - 90
5X-RAY DIFFRACTION2BB91 - 16991 - 169
6X-RAY DIFFRACTION2BB174 - 215174 - 215

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