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- PDB-2ej6: Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2ej6
TitleCrystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound D-proline
Components1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme-inhibitor 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 / 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 / D-PROLINE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.06 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. / Sakamoto, K. / Yokoyama, S. / Tahirov, T.H.
History
DepositionMar 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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)116,04020
Polymers114,2282
Non-polymers1,81218
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-173 kcal/mol
Surface area34660 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)348,12160
Polymers342,6836
Non-polymers5,43754
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 area42510 Å2
ΔGint-531 kcal/mol
Surface area93670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.761, 100.761, 279.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
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 , 5 types, 564 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DPR / D-PROLINE


Type: D-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 30% MPD, 50MM SODIUM CITRATE/HCL, PH5.2; THEN SOAKED IN 30% MPD,50mM D-proline, 50MM SODIUM Acetate, PH5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 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: 2.05→25 Å / Num. all: 65727 / Num. obs: 65727 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.091 / Net I/σ(I): 19
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4 / Num. unique all: 6575 / Rsym value: 0.414 / % possible all: 100

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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
Starting model: PDB ENTRY 2bhp

2bhp


Resolution: 2.06→24.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.64 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23106 3196 5.1 %RANDOM
Rwork0.16996 ---
obs0.17312 60007 95.85 %-
all-60007 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.06→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8076 0 122 546 8744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0228439
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.97511450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06351032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38322.974390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.832151361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7811575
X-RAY DIFFRACTIONr_chiral_restr0.1210.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026467
X-RAY DIFFRACTIONr_nbd_refined0.210.24199
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2608
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.215
X-RAY DIFFRACTIONr_mcbond_it0.9161.55149
X-RAY DIFFRACTIONr_mcangle_it1.57628270
X-RAY DIFFRACTIONr_scbond_it2.9333410
X-RAY DIFFRACTIONr_scangle_it4.6454.53177
LS refinement shellResolution: 2.056→2.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 224 -
Rwork0.258 4071 -
obs-4295 88.08 %

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