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- PDB-1j93: Crystal Structure and Substrate Binding Modeling of the Uroporphy... -

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Basic information

Entry
Database: PDB / ID: 1j93
TitleCrystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism
ComponentsUROPORPHYRINOGEN DECARBOXYLASE
KeywordsLYASE / beta barrel / plastidial enzyme / crystallographic dimer
Function / homology
Function and homology information


uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / chloroplast
Similarity search - Function
Uroporphyrinogen decarboxylase HemE / Uroporphyrinogen decarboxylase signature 1. / Uroporphyrinogen decarboxylase signature 2. / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen decarboxylase, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMartins, B.M. / Grimm, B. / Mock, H.-P. / Huber, R. / Messerschmidt, A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism
Authors: Martins, B.M. / Grimm, B. / Mock, H.-P. / Huber, R. / Messerschmidt, A.
History
DepositionMay 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UROPORPHYRINOGEN DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6686
Polymers39,1871
Non-polymers4805
Water4,161231
1
A: UROPORPHYRINOGEN DECARBOXYLASE
hetero molecules

A: UROPORPHYRINOGEN DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,33512
Polymers78,3752
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)158.44, 158.44, 67.68
Angle α, β, γ (deg.)90, 90, 120
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-585-

SO4

21A-587-

SO4

31A-519-

HOH

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Components

#1: Protein UROPORPHYRINOGEN DECARBOXYLASE / UROD


Mass: 39187.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: Q42967, uroporphyrinogen decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: ammonium sulfate, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-3 mg/mlprotein1drop
210 mMTris-HCl1drop
31.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→18 Å / Num. all: 257709 / Num. obs: 22173 / % possible obs: 97.7 % / Redundancy: 2.14 % / Rsym value: 0.06 / Net I/σ(I): 26.1
Reflection shellResolution: 2.3→18 Å / Redundancy: 3.95 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 257709 / Rsym value: 0.346 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 257709 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Lowest resolution: 2.34 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.346

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1uro

1uro


Resolution: 2.3→18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction option in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 -5 %random
Rwork0.209 ---
obs-21792 97.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 25 231 2953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.225
X-RAY DIFFRACTIONc_bond_d0.007
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2SO4.par
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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