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- PDB-2q2o: Crystal structure of H183C Bacillus subtilis ferrochelatase in co... -

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Basic information

Entry
Database: PDB / ID: 2q2o
TitleCrystal structure of H183C Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride
ComponentsFerrochelatase
KeywordsLYASE / ROSSMANN FOLD / PI-HELIX
Function / homology
Function and homology information


coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature. / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX 2,4-DISULFONIC ACID / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarlberg, T. / Thorvaldsen, O.H. / Al-Karadaghi, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues
Authors: Karlberg, T. / Hansson, M.D. / Yengo, R.K. / Johansson, R. / Thorvaldsen, H.O. / Ferreira, G.C. / Hansson, M. / Al-Karadaghi, S.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9213
Polymers35,2241
Non-polymers6972
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 49.700, 116.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Ferrochelatase / / E.C.4.99.1.1 / Protoheme ferro-lyase / Heme synthetase


Mass: 35223.504 Da / Num. of mol.: 1 / Mutation: H183C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Plasmid: pH183A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32396, protoporphyrin ferrochelatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-H01 / PROTOPORPHYRIN IX 2,4-DISULFONIC ACID / 3,3'-(3,7,12,17-TETRAMETHYL-8,13-DISULFO-22,24-DIHYDROPORPHYRIN-2,18-DIYL)DIPROPANOIC ACID


Mass: 672.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H32N4O10S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, 0.1M spermin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.00903 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 2006
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00903 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 16701 / Num. obs: 16576 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.062 / Net I/σ(I): 16.42
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 6.56 / Num. unique all: 2595 / Rsym value: 0.224 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ProDCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.474 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 836 5 %RANDOM
Rwork0.185 ---
obs0.186 16701 100 %-
all-16701 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---1.86 Å20 Å2
3---2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 47 144 2652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222590
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9893535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69725126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49415429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9071511
X-RAY DIFFRACTIONr_chiral_restr0.1330.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022011
X-RAY DIFFRACTIONr_nbd_refined0.2380.21225
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.28
X-RAY DIFFRACTIONr_mcbond_it1.3291.51605
X-RAY DIFFRACTIONr_mcangle_it1.86222492
X-RAY DIFFRACTIONr_scbond_it3.11431170
X-RAY DIFFRACTIONr_scangle_it4.594.51040
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 61 -
Rwork0.174 1152 -
obs-1213 100 %
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)
11.7082-0.6043-0.30122.80651.05491.1090.03940.2321-0.14970.0321-0.10210.13860.0287-0.20080.0627-0.10680.0193-0.0204-0.0451-0.0282-0.17742.8089-11.2706-16.2806
22.5478-0.8496-1.07662.83921.11261.93540.1942-0.10750.56960.05840.1854-0.5104-0.09590.1459-0.3796-0.13770.00250.0195-0.1198-0.06650.008514.44842.0444-10.1405
316.36915.26023.99624.4576-3.49627.55330.4333-0.84220.46130.0992-0.74191.026-0.07940.32640.30860.1058-0.0305-0.08850.11140.04290.1208-2.2105-4.55380.221
4192.7648-88.4533-13.9099187.14730.314888.3342-0.9056-3.49561.3775-0.63210.3283-2.3631-1.6799-3.05390.57730.04470.0621-0.0605-0.00340.0686-0.00331.62145.8848-4.9556
51.3932-0.2078-0.2621.95310.7671.2130.05990.16040.15870.0099-0.0173-0.16670.0221-0.0302-0.04260.02670.0265-0.03640.0194-0.0125-0.06248.1995-7.2932-14.2606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1693 - 168
2X-RAY DIFFRACTION2AA170 - 310169 - 309
3X-RAY DIFFRACTION3AA9001
4X-RAY DIFFRACTION4AA1000
5X-RAY DIFFRACTION4AA9002 - 9007
6X-RAY DIFFRACTION5AA9008 - 9145

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