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- PDB-5eo6: Coproporphyrinogen III oxidase (HemF) from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5eo6
TitleCoproporphyrinogen III oxidase (HemF) from Acinetobacter baumannii
ComponentsCoproporphyrinogen oxidase
KeywordsOXIDOREDUCTASE / SSGCID / Acinetobacter baumannii / Coproporphyrinogen oxidase / oxidase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / cytoplasm
Similarity search - Function
Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, conserved site / Oxygen-dependent coproporphyrinogen III oxidase superfamily / Coproporphyrinogen III oxidase / Coproporphyrinogen III oxidase signature. / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / coproporphyrinogen oxidase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of oproporphyrinogen III oxidase (aerobic) from Acinetobacter baumannii
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coproporphyrinogen oxidase
B: Coproporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9764
Polymers74,8582
Non-polymers1182
Water14,790821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.140, 97.160, 71.260
Angle α, β, γ (deg.)90.000, 115.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coproporphyrinogen oxidase


Mass: 37428.809 Da / Num. of mol.: 2 / Fragment: AcbaC.17085.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hemF, ABUW_0377, ACX61_01995, AKG96_15100 / Plasmid: AcbaC.17085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D5YE19, coproporphyrinogen oxidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.97 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25.75 mg/mL AcbaC.17085.a.B1.PS02404 with Rigaku Reagents JCSG+ a4: 30% MPD, 20 mM calcium chloride, 100 mM sodium acetate / acetic acid, pH 4.6, cryoprotection: direct, tray 263906a4, puck fyy9-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 154253 / Num. obs: 153349 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.75 % / Biso Wilson estimate: 13.57 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Χ2: 0.996 / Net I/σ(I): 15.31 / Num. measured all: 575739
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
1.45-1.493.670.8280.4862.734162911364113330.56999.7
1.49-1.530.8740.3843.54097410995109750.44899.8
1.53-1.570.9040.3234.154022710770107430.37799.7
1.57-1.620.9430.2465.383956110566105330.28799.7
1.62-1.670.9590.2036.483803910138101090.23799.7
1.67-1.730.9730.1618.0437039983798150.18899.8
1.73-1.80.9820.1319.7535682947494400.15399.6
1.8-1.870.9870.10711.834396913990870.12599.4
1.87-1.960.9910.08714.1532954874586990.10299.5
1.96-2.050.9940.0717.3531469837383120.08199.3
2.05-2.160.9960.05720.7929940799579210.06799.1
2.16-2.290.9950.05223.1528145752174790.0699.4
2.29-2.450.9960.04525.3826577712170610.05399.2
2.45-2.650.9970.04127.7524574659065330.04899.1
2.65-2.90.9970.03730.1722725607060220.04399.2
2.9-3.240.9980.03333.1920660555454990.03999
3.24-3.740.9980.03135.7518083487948290.03699
3.74-4.590.9980.02936.9715105409040510.03399
4.59-6.480.9980.02837.211941323932040.03298.9
6.480.9990.02636.356019179317040.03195

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
ARPmodel building
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VJU chain A

1vju


Resolution: 1.45→50 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1679 2114 1.38 %Random selection
Rwork0.1353 151201 --
obs0.1358 153315 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.01 Å2 / Biso mean: 22.4336 Å2 / Biso min: 7.62 Å2
Refinement stepCycle: final / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 8 827 5762
Biso mean--11.4 34.3 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135201
X-RAY DIFFRACTIONf_angle_d1.177106
X-RAY DIFFRACTIONf_chiral_restr0.102727
X-RAY DIFFRACTIONf_plane_restr0.009946
X-RAY DIFFRACTIONf_dihedral_angle_d14.3651894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48370.22851420.179610087X-RAY DIFFRACTION100
1.4837-1.52080.19581290.162610034X-RAY DIFFRACTION100
1.5208-1.5620.19991310.15510082X-RAY DIFFRACTION100
1.562-1.60790.18441590.135610065X-RAY DIFFRACTION100
1.6079-1.65980.16831130.131110097X-RAY DIFFRACTION100
1.6598-1.71910.15651320.121710110X-RAY DIFFRACTION100
1.7191-1.78790.15221830.115910031X-RAY DIFFRACTION100
1.7879-1.86920.15971520.118210059X-RAY DIFFRACTION100
1.8692-1.96780.15771570.125310054X-RAY DIFFRACTION100
1.9678-2.0910.1681330.126110097X-RAY DIFFRACTION99
2.091-2.25230.17661310.129910037X-RAY DIFFRACTION99
2.2523-2.47880.1841360.134210081X-RAY DIFFRACTION99
2.4788-2.83690.15681500.138510082X-RAY DIFFRACTION99
2.8369-3.57230.1476880.138210168X-RAY DIFFRACTION99
3.5723-500.16871780.1410117X-RAY DIFFRACTION99

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