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- PDB-4un1: Sirohaem decarboxylase AhbA/B - an enzyme with structural homolog... -

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Basic information

Entry
Database: PDB / ID: 4un1
TitleSirohaem decarboxylase AhbA/B - an enzyme with structural homology to the Lrp/AsnC transcription factor family that is part of the alternative haem biosynthesis pathway.
Components(PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


siroheme decarboxylase / heme biosynthetic process / lyase activity
Similarity search - Function
Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / AsnC-type helix-turn-helix domain / : / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
12,18-DIDECARBOXY-SIROHEME / Siroheme decarboxylase alpha subunit / Siroheme decarboxylase beta subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPalmer, D.J. / Brown, D.G. / Warren, M.J. / Pickersgill, R.W.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: The Structure, Function and Properties of Sirohaem Decarboxylase - an Enzyme with Structural Homology to a Transcription Factor Family that is Part of the Alternative Haem Biosynthesis Pathway.
Authors: Palmer, D.J. / Schroeder, S. / Lawrence, A.D. / Deery, E. / Lobo, S.A. / Saraiva, L.M. / Mclean, K.J. / Munro, A.W. / Ferguson, S.J. / Pickersgill, R.W. / Brown, D.G. / Warren, M.J.
History
DepositionMay 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
B: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
C: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
D: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3096
Polymers78,6514
Non-polymers1,6572
Water5,837324
1
A: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
B: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1543
Polymers39,3262
Non-polymers8291
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-33.3 kcal/mol
Surface area14960 Å2
MethodPISA
2
C: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
D: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1543
Polymers39,3262
Non-polymers8291
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-29.9 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.300, 78.600, 150.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY / AHBA DECARBOXYLASE A CHAIN


Mass: 19212.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO DESULFURICANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J364
#2: Protein PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY / AHBB DECARBOXYLASE B CHAIN


Mass: 20112.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO DESULFURICANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J3A4
#3: Chemical ChemComp-OBV / 12,18-DIDECARBOXY-SIROHEME


Mass: 828.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H44FeN4O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsENZYMATICALLY SYNTHESISED USING METHODS AS DESCRIBED IN SCHUBERT ET AT EMBO J 21:2068-2075 (2002)

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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: 2.08 Å3/Da / Density % sol: 40.77 % / Description: NONE
Crystal growpH: 5
Details: 0.1M SODIUM ACETATE PH5, 0.2M AMMONIUM ACETATE, 30% PEG 4000, 0.01M BACL2, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9729978
DetectorDate: Apr 8, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729978 Å / Relative weight: 1
ReflectionResolution: 1.97→44 Å / Num. obs: 46648 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.38
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.5 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZD

4czd


Resolution: 1.97→45.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.646 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. CHAINS C & D NCS OF A AND B, DATA NOT SUBMITTED DUE TO TIME CONSTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25732 2333 5 %RANDOM
Rwork0.20215 ---
obs0.2049 44314 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 114 324 5119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194903
X-RAY DIFFRACTIONr_bond_other_d0.0010.024681
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.9956677
X-RAY DIFFRACTIONr_angle_other_deg0.981310759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77723.538212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02515825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8361538
X-RAY DIFFRACTIONr_chiral_restr0.1360.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215538
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021104
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7692.6212396
X-RAY DIFFRACTIONr_mcbond_other2.7682.622395
X-RAY DIFFRACTIONr_mcangle_it4.2433.912988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4123.0352507
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 165 -
Rwork0.259 3136 -
obs--97 %
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)
10.68211.05630.33952.29740.99721.0640.01620.0856-0.01-0.13470.0304-0.0626-0.0847-0.0086-0.04650.04990.010.00290.05660.01320.0946-22.0228.45620.029
20.5342-0.1077-0.0142.9796-0.28330.73980.06190.06950.0603-0.2609-0.0308-0.0486-0.1321-0.1105-0.03110.07880.03180.01890.1018-0.0060.0554-26.09913.74421.271
30.37080.65380.19752.15390.7261.0547-0.0845-0.04690.0325-0.11580.13510.01740.03090.0618-0.05050.04690.05520.00920.11740.01860.0657-2.489-12.72620.837
40.2418-0.2034-0.22522.04321.15170.7391-0.0303-0.00570.036-0.04010.0181-0.0447-0.00230.0150.01220.04820.0038-0.00440.07440.03250.09242.39-19.02320.086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 166
2X-RAY DIFFRACTION2B1 - 159
3X-RAY DIFFRACTION3C24 - 162
4X-RAY DIFFRACTION4D3 - 159

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