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- PDB-4ch7: Crystal structure of the siroheme decarboxylase NirDL -

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Basic information

Entry
Database: PDB / ID: 4ch7
TitleCrystal structure of the siroheme decarboxylase NirDL
ComponentsNIRD-LIKE PROTEIN
KeywordsTRANSCRIPTION / BIFUNCTIONAL ENZYME / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


siroheme decarboxylase / lyase activity
Similarity search - Function
Arc Repressor Mutant, subunit A - #2890 / Alpha-Beta Plaits - #3460 / Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / : / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #2890 / Alpha-Beta Plaits - #3460 / Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / : / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Siroheme decarboxylase
Similarity search - Component
Biological speciesHYDROGENOBACTER THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsSchmelz, S. / Kriegler, T.M. / Haufschildt, K. / Layer, G. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Crystal Structure of Siroheme Decarboxylase in Complex with Iron-Uroporphyrin III Reveals Two Essential Histidine Residues
Authors: Haufschildt, K. / Schmelz, S. / Kriegler, T.M. / Neumann, A. / Streif, J. / Arai, H. / Heinz, D.W. / Layer, G.
History
DepositionNov 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NIRD-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,2731
Polymers40,2731
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.350, 72.090, 51.200
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NIRD-LIKE PROTEIN / NIRDL


Mass: 40273.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HYDROGENOBACTER THERMOPHILUS (bacteria)
Strain: TK-6 / Description: DSM-6534 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3DFS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growDetails: 19.0% PEG 3350, 0.1M NACIT PH 5.6, 6.7 MM 4-AMINOBENZOIC ACID, 180 MM LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→24.3 Å / Num. obs: 24244 / % possible obs: 98.6 % / Observed criterion σ(I): 2.4 / Redundancy: 4.5 % / Biso Wilson estimate: 42.25 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.002→24.31 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 35.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1213 5 %
Rwork0.2252 --
obs0.2277 24240 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.002→24.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 0 72 2607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032597
X-RAY DIFFRACTIONf_angle_d0.7663494
X-RAY DIFFRACTIONf_dihedral_angle_d14.007991
X-RAY DIFFRACTIONf_chiral_restr0.051391
X-RAY DIFFRACTIONf_plane_restr0.002441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0023-2.08250.35521290.31072452X-RAY DIFFRACTION97
2.0825-2.17720.39731350.29672547X-RAY DIFFRACTION99
2.1772-2.29190.38091330.29642539X-RAY DIFFRACTION99
2.2919-2.43530.3191350.27782551X-RAY DIFFRACTION99
2.4353-2.62320.31881340.27912559X-RAY DIFFRACTION99
2.6232-2.88680.32221360.26172575X-RAY DIFFRACTION100
2.8868-3.30360.30981360.24962585X-RAY DIFFRACTION100
3.3036-4.15880.22191360.20382589X-RAY DIFFRACTION100
4.1588-24.31190.23331390.18482630X-RAY DIFFRACTION99

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