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

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Basic information

Entry
Database: PDB / ID: 2bjk
TitleCrystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD and citrate.
Components1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / DEHYROGENASE
Function / homology
Function and homology information


1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 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. / Aldehyde dehydrogenase domain ...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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsInagaki, E. / Tahirov, T.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase.
Authors: Inagaki, E. / Ohshima, N. / Takahashi, H. / Kuroishi, C. / Yokoyama, S. / Tahirov, T.H.
History
DepositionFeb 4, 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

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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)117,06717
Polymers114,2282
Non-polymers2,84015
Water24,5181361
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)351,20251
Polymers342,6836
Non-polymers8,51945
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
MethodPQS
Unit cell
Length a, b, c (Å)102.436, 102.436, 278.559
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: (0.97687, -0.21369, -0.00718), (-0.2137, -0.9769, 0.00025), (-0.00707, 0.00129, -0.99997)
Vector: 8.28299, 69.34957, 223.04805)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 57113.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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, 1376 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


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


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1361 / 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: 50.1 %
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 32% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD AND 10MM MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8
DetectorType: RIGAKU RAXIS-V / Detector: IMAGE PLATE / Date: Oct 22, 2002 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 511404 / % possible obs: 97.6 % / Observed criterion σ(I): -0.5 / Redundancy: 2.5 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.04→1.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.7 / % possible all: 94

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Processing

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

1uzb


Resolution: 1.4→33.29 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1404023.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.17 6244 2.9 %RANDOM
Rwork0.156 ---
obs0.156 211739 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5273 Å2 / ksol: 0.32476 e/Å3
Displacement parametersBiso mean: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.74 Å20 Å2
2--1.14 Å20 Å2
3----2.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.4→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8076 0 188 1361 9625
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.811.5
X-RAY DIFFRACTIONc_mcangle_it1.152
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 1009 2.9 %
Rwork0.178 33949 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_MODSH1E.PARAMPROTEIN_OCYS_CEA014.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SOL.PARSOL.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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