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- PDB-2xu2: Crystal Structure of the hypothetical protein PA4511 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2xu2
TitleCrystal Structure of the hypothetical protein PA4511 from Pseudomonas aeruginosa
ComponentsUPF0271 PROTEIN PA4511
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / carbohydrate metabolic process / ATP binding
Similarity search - Function
LamB/YcsF/PxpA-like / LamB/YcsF family / Glycoside hydrolase/deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 5-oxoprolinase subunit A 3
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili C, D. / Botting, H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionOct 14, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionJan 19, 2011ID: 2X5E
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0271 PROTEIN PA4511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3882
Polymers27,1961
Non-polymers1921
Water1,45981
1
A: UPF0271 PROTEIN PA4511
hetero molecules

A: UPF0271 PROTEIN PA4511
hetero molecules

A: UPF0271 PROTEIN PA4511
hetero molecules

A: UPF0271 PROTEIN PA4511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5528
Polymers108,7844
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area9270 Å2
ΔGint-49.7 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.830, 90.830, 118.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein UPF0271 PROTEIN PA4511


Mass: 27195.926 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9HVR0
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDUE TO CLONING THE FIRST M IS REMOVED AND REPLACED BY GA

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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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 9
Details: 42.4% PEGMME550, 0.13 M AMMONIUM CITRATE, 0.1M CHES, PH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 9, 2008 / Details: SI (III)
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→21.26 Å / Num. obs: 10668 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DFA

2dfa


Resolution: 2.3→21.26 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.808 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24032 537 4.8 %RANDOM
Rwork0.19166 ---
obs0.19407 10668 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 13 81 1896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211870
X-RAY DIFFRACTIONr_bond_other_d0.0010.021251
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9822543
X-RAY DIFFRACTIONr_angle_other_deg0.8433025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68523.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1211518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 34 -
Rwork0.204 --
obs--99.75 %
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)
119.1030.39517.6420.91430.29353.07780.06860.26980.2222-0.5452-0.148-0.0047-0.04990.08050.07950.37640.0089-0.05070.25960.05020.116333.7873.72512.574
21.41450.14080.00061.4918-0.31231.59310.0632-0.0950.068-0.33630.05140.1875-0.0112-0.0884-0.11450.1939-0.0762-0.05760.14820.01910.189329.4365.17122.302
30.5662-1.2251-0.91883.02312.66234.37110.00050.0057-0.2501-0.16880.02020.57880.1496-0.37-0.02070.1929-0.1206-0.15980.20660.02970.36216.147-3.4819.822
45.99690.41730.00865.64060.67213.02440.14060.4163-0.4216-0.1615-0.2466-0.0470.2909-0.01330.1060.2789-0.05-0.16250.2041-0.06020.194722.072-9.5056.619
51.78671.0293-1.92440.5946-1.10192.1009-1.54282.0471-0.3281-0.8881.2344-0.20931.8049-2.14150.30841.7573-1.5888-0.01082.4876-0.56670.316228.0061.25-0.591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 24
2X-RAY DIFFRACTION2A25 - 144
3X-RAY DIFFRACTION3A145 - 182
4X-RAY DIFFRACTION4A183 - 235
5X-RAY DIFFRACTION5A236 - 248

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