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- PDB-2bja: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 2bja
TitleCrystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NADH
Components1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / DEHYROGENASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / cytoplasmic side of plasma membrane / nucleotide binding
Similarity search - Function
1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsInagaki, E. / Tahirov, T.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Thermus Thermophilus Delta1-Pyrroline-5-Carboxylate Dehydrogenase.
Authors: Inagaki, E. / Ohshima, N. / Takahashi, H. / Kuroishi, C. / Yokoyama, S. / Tahirov, T.H.
History
DepositionFeb 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
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

Downloads & links

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Assembly

Deposited unit
A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,01210
Polymers114,2602
Non-polymers1,7528
Water14,556808
1
A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules

A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules

A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,03630
Polymers342,7796
Non-polymers5,25724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area33640 Å2
ΔGint-118 kcal/mol
Surface area118090 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.007, 102.007, 278.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97656, -0.21521, -0.00416), (-0.21521, -0.97657, 0.00011), (-0.00409, 0.00079, -0.99999)
Vector: 7.97701, 69.1328, 222.82058)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE


Mass: 57129.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OXIDATION OF CYS TO CSO (S-HYDROXYL -CYSTEINE) AT A 322 AND B 322
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SI02, EC: 1.5.1.12

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Non-polymers , 6 types, 816 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.5 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 36% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD,CA.5MM DELTA1-PYRROLINE-5 CARBOXYLATE AND 50 MM SODIUM ACETATE/HCL, PH 5.2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 14, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 85247 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.26
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.15 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZB

1uzb


Resolution: 1.9→37.29 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 397651.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE CISPEPS AT A154-155 AND B154-155.NAHS ARE DISORDERED. MOST PARTS OF DISORDERED REGIONS OF NAHS COULD NOT BE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4178 5.1 %RANDOM
Rwork0.176 ---
obs0.176 82153 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.5945 Å2 / ksol: 0.418808 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.15 Å23.96 Å20 Å2
2--6.15 Å20 Å2
3----12.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 80 808 8963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 650 5.1 %
Rwork0.307 12060 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_OCYS_REP_CSO014.PARAMPROTEIN_OCYS_CSO014.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
X-RAY DIFFRACTION5SOL.PARSOL.TOP

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