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- PDB-2q2n: Crystal structure of Bacillus subtilis ferrochelatase in complex ... -

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Basic information

Entry
Database: PDB / ID: 2q2n
TitleCrystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride
ComponentsFerrochelatase
KeywordsTRANSFERASE / 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: 1.8 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, O.H. / Ferreira, G.C. / Hansson, M. / Al-Karadaghi, S.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 1.4Aug 30, 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_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_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_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

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Assembly

Deposited unit
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9804
Polymers35,2591
Non-polymers7213
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.300, 49.900, 118.200
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: 35258.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32396, protoporphyrin ferrochelatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, 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 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2006
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→29.553 Å / Num. obs: 25719 / % possible obs: 94.1 % / Observed criterion σ(I): 5.5 / Redundancy: 8.1 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.082 / Net I/σ(I): 21.72
Reflection shellResolution: 1.76→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.55 / Num. unique all: 7021 / Rsym value: 0.306 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C1H

1c1h


Resolution: 1.8→29.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.364 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1281 5 %RANDOM
Rwork0.192 ---
obs0.194 25617 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---1.37 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 48 269 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222619
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9923579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2015310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32924.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9991512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022026
X-RAY DIFFRACTIONr_nbd_refined0.1980.21299
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.231
X-RAY DIFFRACTIONr_mcbond_it0.7641.51593
X-RAY DIFFRACTIONr_mcangle_it1.222504
X-RAY DIFFRACTIONr_scbond_it2.05531191
X-RAY DIFFRACTIONr_scangle_it3.0424.51068
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 95 -
Rwork0.266 1814 -
obs-1909 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)
11.1191-0.9519-0.02983.6725-0.58090.4088-0.0019-0.0461-0.0158-0.1920.05860.06050.0804-0.0056-0.0567-0.0592-0.027-0.0499-0.06590.0263-0.063113.5922-13.826514.573
20.66340.1687-0.01222.1659-0.3650.8558-0.00170.0230.1032-0.14850.09890.2313-0.0522-0.0759-0.0971-0.0499-0.0111-0.0503-0.07480.0276-0.029310.17911.817210.2829
37.3249-3.53050.92044.01881.43281.63520.64040.60970.123-0.5152-0.1602-1.0228-0.7667-0.7121-0.48020.0274-0.00080.02840.0184-0.07330.056827.0581-4.63930.1297
457.1952-4.05578.7210.2876-0.61841.3298-0.20931.45571.2015-0.93230.6915-0.32920.72650.8554-0.48220.029-0.04-0.03210.0175-0.01940.00722.82785.52475.3556
50.63090.1115-0.14411.1912-0.21790.5882-0.0140.00810.0053-0.06270.0220.03510.0387-0.0172-0.008-0.0298-0.0138-0.0543-0.00440.0212-0.043717.3116-6.225314.2864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A103 - 169
2X-RAY DIFFRACTION2A170 - 310
3X-RAY DIFFRACTION3A9001
4X-RAY DIFFRACTION4A1000
5X-RAY DIFFRACTION5A9014 - 9270

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