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- PDB-4wsh: Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD... -

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Basic information

Entry
Database: PDB / ID: 4wsh
TitleCrystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / SSGCID / Pseudomonas aeruginosa / Uroporphyrinogen decarboxylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


protoporphyrinogen IX biosynthetic process from glutamate / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / heme biosynthetic process / cytosol
Similarity search - Function
Uroporphyrinogen decarboxylase HemE / Uroporphyrinogen decarboxylase signature 1. / Uroporphyrinogen decarboxylase signature 2. / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase
B: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,66813
Polymers79,7332
Non-polymers93511
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-168 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.760, 73.880, 141.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uroporphyrinogen decarboxylase / URO-D


Mass: 39866.500 Da / Num. of mol.: 2 / Fragment: PsaeA.01152.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hemE, PA5034 / Plasmid: PsaeA.01152.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95458, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Microlytics , MCSG1 F10: 2M Ammonium sulphate, 100mM Tris/HCl pH 8.5; PsaeA.01152.a.B1.PS2161 at 32mg/ml; cryo: 25% in two steps; tray 257913f10, puck dxo7-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 55710 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 32.18 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.051 / Rsym value: 0.045 / Χ2: 0.973 / Net I/σ(I): 20.32 / Num. measured all: 263809
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-24.80.7920.5572.6519482407440700.62799.9
2-2.060.8550.4233.4418974397839740.47699.9
2.06-2.120.9230.3164.6118402386438550.35599.8
2.12-2.180.9530.2515.7117907375137460.28299.9
2.18-2.250.9660.2066.9717470366236540.23299.8
2.25-2.330.9760.1628.8716760351035050.18299.9
2.33-2.420.9820.13410.6516345341034030.15199.8
2.42-2.520.990.10612.8715689327632690.11999.8
2.52-2.630.9930.08815.4515161317631730.09999.9
2.63-2.760.9960.06619.4614434302630200.07599.8
2.76-2.910.9970.05622.7413773288428840.063100
2.91-3.080.9980.04528.3213044274327410.0599.9
3.08-3.30.9990.03534.6612224258125750.03999.8
3.3-3.560.9990.02941.0911287240924010.03399.7
3.56-3.90.9990.02646.8810270222922200.02999.6
3.9-4.360.9990.02352.559325202720140.02699.4
4.36-5.030.9990.02154.678228179817860.02499.3
5.03-6.170.9990.02153.487060155815420.02499
6.17-8.7210.01955.325326121811990.02298.4
8.720.9990.01956.7826487386790.02292

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.95→39.489 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 2854 5.14 %Random selection
Rwork0.1583 52699 --
obs0.1605 55553 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.78 Å2 / Biso mean: 36.6565 Å2 / Biso min: 16.76 Å2
Refinement stepCycle: final / Resolution: 1.95→39.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 47 376 5721
Biso mean--78.41 39.84 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075605
X-RAY DIFFRACTIONf_angle_d1.0257649
X-RAY DIFFRACTIONf_chiral_restr0.042837
X-RAY DIFFRACTIONf_plane_restr0.0051000
X-RAY DIFFRACTIONf_dihedral_angle_d12.1962038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.98360.26881460.23332556270299
1.9836-2.01970.30811470.198326252772100
2.0197-2.05850.24381360.197726122748100
2.0585-2.10060.24471420.18525892731100
2.1006-2.14620.23311370.18426232760100
2.1462-2.19610.25441420.184126002742100
2.1961-2.25110.21631510.172726172768100
2.2511-2.31190.24231260.157926292755100
2.3119-2.37990.23361210.161626402761100
2.3799-2.45680.20181540.158125982752100
2.4568-2.54450.23131520.159925942746100
2.5445-2.64640.2161480.166126532801100
2.6464-2.76680.21761330.166826102743100
2.7668-2.91260.24531420.174926332775100
2.9126-3.09510.25281450.176226602805100
3.0951-3.33390.21511320.17226602792100
3.3339-3.66920.18231680.156626382806100
3.6692-4.19960.15281420.127926792821100
4.1996-5.28910.16391460.12562706285299
5.2891-39.49680.1651440.15772777292198
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)
12.33010.40120.92071.72410.24481.6039-0.014-0.0505-0.0730.1876-0.0040.0680.0143-0.10480.01130.26990.02350.00680.1938-0.02750.242125.889731.610935.7971
20.8783-0.4952-0.01642.61780.93191.36190.11810.0436-0.0214-0.1253-0.0865-0.1919-0.00030.0474-0.00970.1970.0009-0.00710.17180.01320.19534.207918.941630.67
31.0206-0.00710.45691.14680.36682.66450.0079-0.0001-0.00540.0428-0.05540.07020.0326-0.04370.03490.1818-0.0108-0.00170.18450.01760.221523.798419.233123.6247
41.38850.85160.66051.55580.38611.8492-0.02010.02840.2225-0.0372-0.01640.138-0.2478-0.11830.0510.23710.0583-0.01580.1974-0.01890.275220.430540.931824.2392
54.0290.0571-1.24541.3287-0.12840.8484-0.05740.07390.3085-0.10470.1076-0.0071-0.1895-0.0771-0.02430.26930.0379-0.01120.2256-0.00470.184840.034632.0017-12.1315
62.1031-0.9298-1.78242.75150.80892.30110.1774-0.09730.48690.14280.1627-0.4248-0.46720.383-0.31490.3418-0.0313-0.00740.28530.01220.32843.36643.0193-6.7653
72.18170.1911-1.70741.3279-0.113.70520.13260.00250.23560.0723-0.07150.0038-0.48410.0532-0.06550.39350.0434-0.02170.2240.04260.330.670146.3604-0.4428
81.8229-0.4389-0.97822.96120.14212.6964-0.09230.1715-0.0197-0.09170.04510.08130.0997-0.12210.04810.2103-0.0074-0.01920.26250.01930.189926.861124.568-6.0446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 122 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 262 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 355 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 52 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 158 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 262 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 263 through 355 )B0

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