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Basic information

Entry
Database: PDB / ID: 3rjl
TitleCrystal structure of 1-pyrroline-5-carboxylate dehydrogenase from Bacillus licheniformis (Target NYSGRC-000337)
Components1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / PROLINE OXIDATION / REDOX CONTROL / APOPTOSIS / NAD BINDING / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC)
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / glutamate biosynthetic process
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 / : / 1-pyrroline-5-carboxylate dehydrogenase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.2 Å
AuthorsPatskovsky, Y. / Toro, R. / Foti, R. / Seidel, R.D. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase from Bacillus Licheniformis
Authors: Patskovsky, Y. / Toro, R. / Foti, R. / Seidel, R.D. / Almo, S.C.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
C: 1-pyrroline-5-carboxylate dehydrogenase
D: 1-pyrroline-5-carboxylate dehydrogenase
E: 1-pyrroline-5-carboxylate dehydrogenase
F: 1-pyrroline-5-carboxylate dehydrogenase
G: 1-pyrroline-5-carboxylate dehydrogenase
H: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,13163
Polymers476,3758
Non-polymers5,75655
Water12,124673
1
A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61811
Polymers59,5471
Non-polymers1,07110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0566
Polymers59,5471
Non-polymers5095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,78312
Polymers59,5471
Non-polymers1,23711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1687
Polymers59,5471
Non-polymers6216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2278
Polymers59,5471
Non-polymers6807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1157
Polymers59,5471
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2217
Polymers59,5471
Non-polymers6746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9435
Polymers59,5471
Non-polymers3964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

D: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,78618
Polymers119,0942
Non-polymers1,69216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area7000 Å2
ΔGint-69 kcal/mol
Surface area35690 Å2
MethodPISA
10
B: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

C: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,83918
Polymers119,0942
Non-polymers1,74516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area6900 Å2
ΔGint-68 kcal/mol
Surface area35760 Å2
MethodPISA
11
E: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

G: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,44815
Polymers119,0942
Non-polymers1,35513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_446-x-1,y-1/2,-z+11
Buried area6450 Å2
ΔGint-55 kcal/mol
Surface area35620 Å2
MethodPISA
12
F: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

H: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,05812
Polymers119,0942
Non-polymers96410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area6340 Å2
ΔGint-46 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.267, 116.114, 181.768
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROAA4 - 5164 - 516
2THRTHRBB3 - 5163 - 516
3PROPROCC4 - 5164 - 516
4PROPRODD4 - 5164 - 516
5PROPROEE4 - 5164 - 516
6PROPROFF4 - 5164 - 516
7PROPROGG4 - 5164 - 516
8PROPROHH4 - 5164 - 516

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Components

#1: Protein
1-pyrroline-5-carboxylate dehydrogenase / P5C dehydrogenase


Mass: 59546.922 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: ATCC 14580, DSM 13 / Gene: rocA, BLi00374, BL01710 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: Q65NN2, EC: 1.5.1.12
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M SODIUM ACETATE, PH 4.6, 200MM CADMIUM CHLORIDE, 30% PEG400, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 217382 / % possible obs: 87.7 % / Observed criterion σ(I): -5 / Redundancy: 2.9 % / Biso Wilson estimate: 35.083 Å2 / Rsym value: 0.15 / Net I/σ(I): 4.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3QAN

3qan


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.516 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29218 5701 3 %RANDOM
Rwork0.22225 ---
obs0.22433 182882 86.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.82 Å20 Å2-0.2 Å2
2---4.04 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31754 0 79 673 32506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02232540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.95144062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78454123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32724.7481489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.844155478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.53615159
X-RAY DIFFRACTIONr_chiral_restr0.0860.24844
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124875
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.039220439
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.625332927
X-RAY DIFFRACTIONr_scbond_it7.561412101
X-RAY DIFFRACTIONr_scangle_it10.685711123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3919 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.420.5
Bmedium positional0.40.5
Cmedium positional0.390.5
Dmedium positional0.380.5
Emedium positional0.360.5
Fmedium positional0.410.5
Gmedium positional0.340.5
Hmedium positional0.390.5
Amedium thermal6.225
Bmedium thermal5.735
Cmedium thermal5.65
Dmedium thermal6.065
Emedium thermal5.865
Fmedium thermal6.455
Gmedium thermal5.975
Hmedium thermal5.765
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 395 -
Rwork0.373 12562 -
obs--81.96 %

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