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

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Basic information

Entry
Database: PDB / ID: 2bhp
TitleCrystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD.
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 / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-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: 1.8 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
DepositionJan 16, 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.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_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

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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)117,07821
Polymers114,2282
Non-polymers2,85019
Water21,6181200
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)351,23363
Polymers342,6836
Non-polymers8,54957
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)102.179, 102.179, 278.614
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2252-

HOH

21B-2060-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9778, -0.20933, -0.00891), (-0.20934, -0.97784, 5.0E-5), (-0.00872, 0.00182, -0.99996)
Vector: 8.30915, 69.28711, 223.0739)

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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, 1219 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.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


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


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / 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 %
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 32% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 5 MM NAD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 26, 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: 1.8→50 Å / Num. obs: 99097 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 6.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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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: 1.8→44.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 703397.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THERE ARE DISORDERD REGIONS IN NADS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 4781 5.1 %RANDOM
Rwork0.148 ---
obs0.148 94390 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.3375 Å2 / ksol: 0.432719 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å21.07 Å20 Å2
2--1.12 Å20 Å2
3----2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 190 1200 9460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.22 776 5.3 %
Rwork0.191 13770 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.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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