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- PDB-4zr8: Structure of uroporphyrinogen decarboxylase from Acinetobacter ba... -

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Basic information

Entry
Database: PDB / ID: 4zr8
TitleStructure of uroporphyrinogen decarboxylase from Acinetobacter baumannii
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / SSGCID / Acinetobacter baumannii / 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 / 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 speciesAcinetobacter baumannii AB5075 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of uroporphyrinogen decarboxylase from Acinetobacter baumannii
Authors: Abendroth, J. / Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
B: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,43211
Polymers80,9642
Non-polymers4689
Water14,376798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-14 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.540, 83.380, 68.460
Angle α, β, γ (deg.)90.000, 106.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uroporphyrinogen decarboxylase / URO-D


Mass: 40482.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: hemE, A591_A1129 / Plasmid: AcbaC.01152.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0A2T261, UniProt: A0A0M3KL37*PLUS, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2144
22.2144
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, sitting drop7.65native: Microlytics MGSC1 screen, B11: 18% PEG8000, 200 mM magnesium chloride, 100 mM Tris-HCl, pH 7.65, 11 mg/mL AcbaC.001152.a.B1.PW3767 + 2 mM NAD, cryoprotectant: 20% ethylene glycol, tray 262775, puck kzo2-10
2902vapor diffusion, sitting drop6.5iodide: Microlytics MGSC1 screen, A12: 20% PEG4000, 200 mM calcium chloride, 100 mM Tris-HCl, pH 8.5, 11 mg/mL AcbaC.001152.a.B1.PW3767 + 2 mM NAD, cryoprotectant: 10% ethylene glycol + 250 mM sodium iodide, then 20% ethylene glycol + 500 mM sodium iodide, tray 262775, puck hml1-17

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97856
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDApr 16, 2015
RIGAKU SATURN 944+2CCDApr 17, 2015
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
21.54181
ReflectionNumber: 483071 / Rmerge(I) obs: 0.026 / Χ2: 1.88 / D res high: 2 Å / Num. obs: 91083 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.945096710.016
6.328.94180210.016
5.166.32237210.017
4.475.16284710.016
44.47325810.016
3.654366410.017
3.383.65398510.019
3.163.38425810.022
2.983.16453010.024
2.832.98479310.028
2.72.83506110.03
2.582.7531210.034
2.482.58553010.039
2.392.48571710.044
2.312.39595510.047
2.242.31618910.055
2.172.24634510.062
2.112.17646110.064
2.052.11633210.071
22.05570510.085
ReflectionResolution: 1.5→50 Å / Num. obs: 112341 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.13 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.044 / Χ2: 0.998 / Net I/σ(I): 20.9 / Num. measured all: 424436
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.543.730.860.4482.8930961831483010.52499.8
1.54-1.580.9170.3463.7130195807480690.40599.9
1.58-1.630.9330.2844.5329449786178480.33299.8
1.63-1.680.9520.2335.528578763276150.27299.8
1.68-1.730.9690.1896.8327940742474120.2299.8
1.73-1.790.980.1448.8626977715971480.16899.8
1.79-1.860.9870.11810.9626240695069380.13899.8
1.86-1.940.9920.08814.2225039662166070.10399.8
1.94-2.020.9950.06818.124253639663880.07999.9
2.02-2.120.9970.05322.6723180612261040.06199.7
2.12-2.240.9980.04427.0421953577357660.05199.9
2.24-2.370.9980.03930.3421097555355410.04599.8
2.37-2.540.9980.03334.3219690518651680.03999.7
2.54-2.740.9990.02939.1318348482048180.034100
2.74-30.9990.02544.4416935443944260.02999.7
3-3.350.9990.02250.0715284400940000.02699.8
3.35-3.870.9990.01956.2213573357435610.02299.6
3.87-4.740.9990.01859.4211428301730090.02199.7
4.74-6.710.9990.01858.68826235623430.02199.4
6.71-500.9990.01958.664490131412790.02297.3

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.805 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 5705 5.08 %Random selection
Rwork0.129 106613 --
obs0.1306 112318 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.58 Å2 / Biso mean: 22.1475 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.5→28.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 27 805 6254
Biso mean--39.68 33.12 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065730
X-RAY DIFFRACTIONf_angle_d1.0377819
X-RAY DIFFRACTIONf_chiral_restr0.046885
X-RAY DIFFRACTIONf_plane_restr0.0051009
X-RAY DIFFRACTIONf_dihedral_angle_d12.7682114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.2351900.174435543744100
1.5171-1.53490.23271860.165535163702100
1.5349-1.55360.24121880.149135643752100
1.5536-1.57330.19791880.150835143702100
1.5733-1.5940.20691960.147535503746100
1.594-1.61580.19461850.133634883673100
1.6158-1.63890.19891880.129136143802100
1.6389-1.66340.16061800.125135523732100
1.6634-1.68940.18211700.125535343704100
1.6894-1.71710.19351870.126435533740100
1.7171-1.74670.15141790.118435643743100
1.7467-1.77840.17591810.117735463727100
1.7784-1.81260.16612000.12135273727100
1.8126-1.84960.17281770.12135783755100
1.8496-1.88980.16041980.118435553753100
1.8898-1.93380.17841670.111835413708100
1.9338-1.98210.1311860.117935583744100
1.9821-2.03570.16492160.123435463762100
2.0357-2.09560.16012230.122834983721100
2.0956-2.16320.16661990.121235373736100
2.1632-2.24050.161740.119235643738100
2.2405-2.33020.15431840.122135413725100
2.3302-2.43620.15931850.125235933778100
2.4362-2.56450.16412080.128935413749100
2.5645-2.72510.14642040.130135683772100
2.7251-2.93530.16341970.141435383735100
2.9353-3.23030.17561760.140535903766100
3.2303-3.69690.13621880.131235833771100
3.6969-4.65460.13932050.117635903795100
4.6546-28.81030.15522000.14033616381699

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