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- PDB-2h5g: Crystal structure of human pyrroline-5-carboxylate synthetase -

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Basic information

Entry
Database: PDB / ID: 2h5g
TitleCrystal structure of human pyrroline-5-carboxylate synthetase
ComponentsDelta 1-pyrroline-5-carboxylate synthetase
KeywordsOXIDOREDUCTASE / dehydrogenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ornithine biosynthetic process / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / glutamate metabolic process / citrulline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process ...ornithine biosynthetic process / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / glutamate metabolic process / citrulline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / response to temperature stimulus / Mitochondrial protein degradation / mitochondrial inner membrane / mitochondrion / RNA binding / ATP binding / identical protein binding
Similarity search - Function
Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase ...Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 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 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
Delta-1-pyrroline-5-carboxylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsPapagrigoriou, E. / Shafqat, N. / Turnbull, A.P. / Berridge, G. / Hozjan, V. / Kavanagh, K. / Gileadi, O. / Smee, C. / Bray, J. / Gorrec, F. ...Papagrigoriou, E. / Shafqat, N. / Turnbull, A.P. / Berridge, G. / Hozjan, V. / Kavanagh, K. / Gileadi, O. / Smee, C. / Bray, J. / Gorrec, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of human pyrroline-5-carboxylate synthetase
Authors: Papagrigoriou, E. / Shafqat, N. / Turnbull, A.P. / Berridge, G. / Hozjan, V. / Kavanagh, K. / Gileadi, O. / Smee, C. / Bray, J. / Gorrec, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / ...Authors: Papagrigoriou, E. / Shafqat, N. / Turnbull, A.P. / Berridge, G. / Hozjan, V. / Kavanagh, K. / Gileadi, O. / Smee, C. / Bray, J. / Gorrec, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionMay 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Delta 1-pyrroline-5-carboxylate synthetase
B: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0528
Polymers103,4752
Non-polymers5766
Water4,990277
1
A: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules

A: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0528
Polymers103,4752
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7040 Å2
ΔGint-97 kcal/mol
Surface area32790 Å2
MethodPISA, PQS
2
B: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0264
Polymers51,7381
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules

B: Delta 1-pyrroline-5-carboxylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0528
Polymers103,4752
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.022, 137.402, 72.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRVALVAL3AA362 - 53330 - 201
211THRTHRVALVAL3BB362 - 53330 - 201
321MSEMSESERSER3AA551 - 652219 - 320
421MSEMSESERSER3BB551 - 652219 - 320
531LYSLYSPROPRO3AA662 - 790330 - 458
631LYSLYSPROPRO3BB662 - 790330 - 458
112GLNGLNGLUGLU4AA534 - 540202 - 208
212GLNGLNGLUGLU4BB534 - 540202 - 208

NCS ensembles :
ID
1
2
DetailsThe biological unit can be generated if the following symmetry operator is applied to chain A. -x, -y, z 1 0 0

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Components

#1: Protein Delta 1-pyrroline-5-carboxylate synthetase / pyrroline-5-carboxylate synthetase isoform 1 / PYCS / P5CS / Aldehyde dehydrogenase 18 family member A1


Mass: 51737.605 Da / Num. of mol.: 2 / Fragment: Gamma-glutamyl phosphate reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH18A1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta
References: UniProt: P54886, glutamate-5-semialdehyde dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1% PEG 3350, 1.0M (NH4)2SO4, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2005
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.25→91.29 Å / Num. all: 58292 / Num. obs: 57217 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.89 % / Rmerge(I) obs: 0.056 / Rsym value: 0.033
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.39 / Num. unique all: 11978 / Rsym value: 0.205 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→46.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.152 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27211 2890 5.1 %RANDOM
Rwork0.23037 ---
all0.23248 57217 --
obs0.23248 54237 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.168 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20 Å2
2---0.14 Å20 Å2
3---2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 30 277 6655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9718861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46624.194279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.463151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3051545
X-RAY DIFFRACTIONr_chiral_restr0.1050.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024814
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24450
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.2136
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.40934324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.54956720
X-RAY DIFFRACTIONr_scbond_it6.30272446
X-RAY DIFFRACTIONr_scangle_it8.077112141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11612tight positional0.080.05
253medium positional0.280.5
11399loose positional0.255
11612tight thermal0.330.5
253medium thermal1.492
11399loose thermal3.0610
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 197 -
Rwork0.256 3346 -
obs--84.04 %

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