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- PDB-2ehu: Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 2ehu
TitleCrystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine
Components1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme-coenzyme-inhibitor ternary complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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. / 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsInagaki, E. / Sakamoto, K. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Analysis of delta1-pyrroline-5-carboxylate dehydrogenase in ternary complex with inhibitor and NAD.
Authors: Inagaki, E. / Ohshima, N.
History
DepositionMar 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)117,58325
Polymers114,2282
Non-polymers3,35523
Water17,799988
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-195 kcal/mol
Surface area33950 Å2
MethodPISA
2
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)352,75075
Polymers342,6836
Non-polymers10,06669
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 area51950 Å2
ΔGint-610 kcal/mol
Surface area91260 Å2
MethodPISA
3
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)235,16750
Polymers228,4564
Non-polymers6,71146
Water724
TypeNameSymmetry operationNumber
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)102.556, 102.556, 278.585
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-3004-

HOH

21A-3005-

HOH

31B-3009-

HOH

DetailsThe biological assembly would be a dimer in the asymmetric unit.

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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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SI02, EC: 1.5.1.12

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Non-polymers , 6 types, 1011 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.2
Details: 30% MPD, 50MM SODIUM CITRATE/HCL, 30% MPD, 5mM NAD+, 50mM L-serine, 50MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 7, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→92.85 Å / Num. all: 100690 / Num. obs: 100690 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.059 / Net I/σ(I): 33.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.7 / Num. unique all: 10046 / Rsym value: 0.247 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.749 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16725 5024 5 %RANDOM
Rwork0.13863 ---
all0.14006 95665 --
obs0.14006 95665 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8076 0 224 988 9288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228494
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.98911538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07151030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64722.972387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.436151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0531576
X-RAY DIFFRACTIONr_chiral_restr0.0870.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026488
X-RAY DIFFRACTIONr_nbd_refined0.1940.24361
X-RAY DIFFRACTIONr_nbtor_refined0.310.25797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2880
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.238
X-RAY DIFFRACTIONr_mcbond_it0.5461.55146
X-RAY DIFFRACTIONr_mcangle_it1.0528244
X-RAY DIFFRACTIONr_scbond_it2.00333474
X-RAY DIFFRACTIONr_scangle_it3.3974.53294
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 360 -
Rwork0.163 6956 -
obs-7316 98.69 %

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