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- PDB-1x7d: Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed ... -

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Basic information

Entry
Database: PDB / ID: 1x7d
TitleCrystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms
Componentsornithine cyclodeaminase
KeywordsLYASE / Deaminase / Binds NAD+ / Binds L-ornithine / binds L-proline / 2 Helix Bundle / Beta Barrel / Rossmann Fold
Function / homology
Function and homology information


ornithine cyclodeaminase activity / ornithine cyclodeaminase / L-proline biosynthetic process / nucleotide binding
Similarity search - Function
ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-ornithine / Ornithine cyclodeaminase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER/ MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlam, S. / Goodman, J.L. / Wang, S. / Ruzicka, F.J. / Frey, P.A. / Wedekind, J.E.
CitationJournal: Biochemistry / Year: 2004
Title: Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications for the u-Crystallin Family
Authors: Goodman, J.L. / Wang, S. / Alam, S. / Ruzicka, F.J. / Frey, P.A. / Wedekind, J.E.
History
DepositionAug 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ornithine cyclodeaminase
B: ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23715
Polymers77,6962
Non-polymers2,54113
Water14,916828
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-153 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 78.620, 119.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ornithine cyclodeaminase


Mass: 38847.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ORNITHINE CYCLASE (DEAMINATING) / Plasmid: pET-21a(+) and pET-21a-OCD / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) and D834(DE3) / References: UniProt: Q88H32, ornithine cyclodeaminase

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Non-polymers , 6 types, 841 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / pH: 6.25
Details: 0.1 M MES, 40% (v/v) MPD, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON AND GERMANIUM CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.6→24.95 Å / Num. obs: 86668 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 2.29 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 12.2
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.203 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER/ MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U7H

1u7h


Resolution: 1.6→24.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2107943.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4400 5.1 %RANDOM
Rwork0.17 ---
obs0.17 86668 98.6 %-
all-86705 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.49 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.6→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 168 828 6231
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9671.5
X-RAY DIFFRACTIONc_mcangle_it1.4382
X-RAY DIFFRACTIONc_scbond_it1.8762
X-RAY DIFFRACTIONc_scangle_it2.7222.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 699 5.2 %
Rwork0.241 12853 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD_XPLOR.PARNAD_XPLOR.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SUPER1.PARSUPER1.TOP

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