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- PDB-4exq: CRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BU... -

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Basic information

Entry
Database: PDB / ID: 4exq
TitleCRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BURKHOLDERIA THAILANDENSIS E264
ComponentsUroporphyrinogen decarboxylaseUroporphyrinogen III decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / NIH / SBRI / URO-D / HEME BIOSYNTHESIS / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / protoporphyrinogen IX biosynthetic process / cytoplasm
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 speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8642
Polymers39,8411
Non-polymers231
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uroporphyrinogen decarboxylase
hetero molecules

A: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7284
Polymers79,6822
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area2290 Å2
ΔGint-31 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.320, 53.320, 233.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uroporphyrinogen decarboxylase / Uroporphyrinogen III decarboxylase / UPD / URO-D


Mass: 39841.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: hemE, BTH_I3304 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2STF3, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 41883 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.07 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.26
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.462 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2105 5 %RANDOM
Rwork0.178 ---
obs0.179 41768 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 1 174 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192759
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9563771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25722.869122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64315395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7761524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212158
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 130 -
Rwork0.244 2562 -
obs--99.85 %
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)
10.46730.59120.04420.81480.00490.3020.0573-0.0057-0.04430.0265-0.0237-0.0358-0.0625-0.0419-0.03360.1050.00660.00110.0432-0.00650.062316.0418-29.1943-24.1552
20.24010.3689-0.02481.5124-0.26420.16830.0861-0.0052-0.0119-0.006-0.06810.0474-0.08040.0539-0.0180.1604-0.02680.01190.02140.00170.045220.9873-17.2266-24.7295
30.0077-0.0670.04161.06350.41813.6067-0.01320.00410.0177-0.0603-0.0381-0.075-0.39340.22230.05130.1682-0.0161-0.02450.0216-0.00810.073411.9267-9.3342-11.1063
40.07530.20160.54110.54181.4544.1324-0.03860.0134-0.0048-0.09010.036-0.0188-0.19480.22690.00260.11560.0088-0.0020.08740.01050.04713.1961-20.1842-15.4754
50.1424-0.04570.48650.4513-0.33691.7483-0.0043-0.02030.00660.0101-0.00760.0435-0.0474-0.05830.0120.07990.02-0.0010.06890.00470.04566.1079-22.5442-5.8428
60.5371-0.082-0.18210.2149-0.01310.25140.0034-0.053-0.0414-0.00160.01440.01910.01010.0238-0.01780.072-0.0057-0.00030.06140.00260.066517.6013-38.8626-16.8072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 41
2X-RAY DIFFRACTION2A42 - 76
3X-RAY DIFFRACTION3A77 - 135
4X-RAY DIFFRACTION4A136 - 169
5X-RAY DIFFRACTION5A170 - 261
6X-RAY DIFFRACTION6A262 - 358

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