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- PDB-1olt: Coproporphyrinogen III oxidase (HemN) from Escherichia coli is a ... -

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Basic information

Entry
Database: PDB / ID: 1olt
TitleCoproporphyrinogen III oxidase (HemN) from Escherichia coli is a Radical SAM enzyme.
ComponentsOXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE
KeywordsOXIDOREDUCTASE / HEME BIOSYNTHESIS / DECARBOXYLASE / RADICAL SAM ENZYME / 4FE- 4S CLUSTER / S-ADENOSYL-L-METHIONINE
Function / homology
Function and homology information


coproporphyrinogen dehydrogenase / coproporphyrinogen dehydrogenase activity / protoporphyrinogen IX biosynthetic process from glutamate / coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #920 / Oxygen-independent coproporphyrinogen III oxidase HemN / HemN, C-terminal / Anaerobic coproporphyrinogen-III oxidase / HemN C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM ...Arc Repressor Mutant, subunit A - #920 / Oxygen-independent coproporphyrinogen III oxidase HemN / HemN, C-terminal / Anaerobic coproporphyrinogen-III oxidase / HemN C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Oxygen-independent coproporphyrinogen III oxidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsLayer, G. / Moser, J. / Heinz, D.W. / Jahn, D. / Schubert, W.-D.
CitationJournal: Embo J. / Year: 2003
Title: Crystal Structure of Coproporphyrinogen III Oxidase Reveals Cofactor Geometry of Radical Sam Enzymes
Authors: Layer, G. / Moser, J. / Heinz, D.W. / Jahn, D. / Schubert, W.-D.
History
DepositionAug 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9304
Polymers52,7821
Non-polymers1,1493
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.036, 114.036, 76.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2090-

HOH

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Components

#1: Protein OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE / COPROPORPHYRINOGENASE / COPROGEN OXIDASE


Mass: 52781.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12
References: UniProt: P32131, Oxidoreductases; Acting on the CH-CH group of donors
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCARRIES OUT THE ANAEROBIC TRANSFORMATION OF COPROPORPHYRINOGEN-III INTO PROTOPORPHYRINOGEN-IX.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP: 5 MICROL PROTEIN + 5 MICROL RESEVOIR, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.5, 3 MM DTT, 150 MM NACL, 0.01% (V/V) C8E4 RESEVOIR: 22% (W/V) PEG10000, 100 MM HEPES PH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21 mMSAM1drop
322 %PEG100001reservoir
4100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.742
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.742 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 1440548 / % possible obs: 99.1 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.6
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 10.2 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 30 Å / Num. obs: 34220 / Redundancy: 9.4 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 96.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 10.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.07→100 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.246 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1735 5.1 %RANDOM
Rwork0.154 ---
obs0.155 32527 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.07→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 62 396 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0214274
X-RAY DIFFRACTIONr_bond_other_d0.0040.023778
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9715851
X-RAY DIFFRACTIONr_angle_other_deg1.01938843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024986
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02922
X-RAY DIFFRACTIONr_nbd_refined0.3040.21027
X-RAY DIFFRACTIONr_nbd_other0.2550.24811
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1010.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841.52525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4124126
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63831749
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9134.51713
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: 2.07→2.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.215 133
Rwork0.158 2334
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)
15.4623-5.2962-3.38613.73748.9087.891-0.3549-0.0188-0.23290.4860.21810.00020.34680.21530.13670.2104-0.0337-0.07510.36570.0590.266142.632554.632217.9823
20.8363-0.5993-0.08371.77640.09390.79030.00940.02650.1189-0.0226-0.015-0.2781-0.01530.22710.00560.00210.0097-0.0060.08540.00660.044725.399662.3739.0667
33.1313-0.42331.00454.73933.08074.5982-0.01010.0007-0.0964-0.03080.0672-0.41350.17110.5097-0.05710.155-0.0003-0.06450.4760.06580.42152.662262.29317.4329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 33
2X-RAY DIFFRACTION2A34 - 362
3X-RAY DIFFRACTION3A363 - 444
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 59440 / Num. reflection Rfree: 3170
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.215 / Rfactor Rwork: 0.158

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