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- PDB-2amf: Crystal structure of 1-Pyrroline-5-Carboxylate Reductase from Hum... -

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Basic information

Entry
Database: PDB / ID: 2amf
TitleCrystal structure of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen Streptococcus Pyogenes
Components1-Pyrroline-5-Carboxylate reductase
KeywordsOXIDOREDUCTASE / 1-Pyrroline-5-Reductase / Pyrroline-5-Carboxylate Reductase / Pyrroline Reductase / Proline biosynthesis / NAD(P)binding protein / Rossmann Fold / Domain swapping / human pathogen / Streptococcus pyogenes / Structural Genomics / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
ProC C-terminal domain-like / ProC C-terminal domain-like fold / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROLINE / : / Pyrroline-5-carboxylate reductase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to 2AHR / Resolution: 2.2 Å
AuthorsNocek, B. / Lezondra, L. / Holzle, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Delta(1)-Pyrroline-5-carboxylate Reductase from Human Pathogens Neisseria meningitides and Streptococcus pyogenes
Authors: Nocek, B. / Chang, C. / Li, H. / Lezondra, L. / Holzle, D. / Collart, F. / Joachimiak, A.
History
DepositionAug 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: 1-Pyrroline-5-Carboxylate reductase
B: 1-Pyrroline-5-Carboxylate reductase
C: 1-Pyrroline-5-Carboxylate reductase
D: 1-Pyrroline-5-Carboxylate reductase
E: 1-Pyrroline-5-Carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,29120
Polymers138,0255
Non-polymers1,26615
Water13,313739
1
A: 1-Pyrroline-5-Carboxylate reductase
B: 1-Pyrroline-5-Carboxylate reductase
C: 1-Pyrroline-5-Carboxylate reductase
D: 1-Pyrroline-5-Carboxylate reductase
E: 1-Pyrroline-5-Carboxylate reductase
hetero molecules

A: 1-Pyrroline-5-Carboxylate reductase
B: 1-Pyrroline-5-Carboxylate reductase
C: 1-Pyrroline-5-Carboxylate reductase
D: 1-Pyrroline-5-Carboxylate reductase
E: 1-Pyrroline-5-Carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,58240
Polymers276,05010
Non-polymers2,53330
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area58140 Å2
ΔGint-601 kcal/mol
Surface area88170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)171.822, 109.960, 84.158
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-4447-

HOH

21E-4501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 256 / Label seq-ID: 4 - 259

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
1-Pyrroline-5-Carboxylate reductase


Mass: 27604.986 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: proC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 13621418, UniProt: Q9A1S9*PLUS, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPRO 4240, 4330 and NA 850 are associated with protein chain A PRO 4241, 4331 and NA 851 are ...PRO 4240, 4330 and NA 850 are associated with protein chain A PRO 4241, 4331 and NA 851 are associated with protein chain B PRO 4242, 4332 and NA 852 are associated with protein chain C PRO 4243, 4333 and NA 853 are associated with protein chain D PRO 4244, 4334 and NA 854 are associated with protein chain E

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5 M sodium formate, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 80125 / Num. obs: 78923 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.326 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-CollectCollectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: isomorphous to 2AHR
Starting model: pdb entry 2AHR

2ahr


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.766 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21542 3930 5 %RANDOM
Rwork0.17333 ---
all0.17549 78246 --
obs0.17549 74316 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.756 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20.25 Å2
2---0.43 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9619 0 85 739 10443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229835
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.99713294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70251282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7625.706326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.936151807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1121530
X-RAY DIFFRACTIONr_chiral_restr0.0870.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.24919
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.26915
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2748
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_it0.5011.56471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.953210421
X-RAY DIFFRACTIONr_scbond_it1.79933379
X-RAY DIFFRACTIONr_scangle_it2.9564.52873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1911 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.480.5
2Bmedium positional0.40.5
3Cmedium positional0.450.5
4Dmedium positional0.430.5
5Emedium positional0.370.5
1Amedium thermal0.562
2Bmedium thermal0.532
3Cmedium thermal0.652
4Dmedium thermal0.512
5Emedium thermal0.662
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 238 -
Rwork0.222 5041 -
obs--90.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4036-0.2328-0.32690.1980.01770.7225-0.02470.0389-0.05890.02050.0484-0.0202-0.0709-0.1083-0.0237-0.04390.0075-0.00890.0071-0.0197-0.010348.608784.444254.6274
20.00550.05730.01570.69150.44570.86190.06510.057-0.04190.0731-0.11740.031-0.0876-0.08610.05230.02440.00750.0048-0.0461-0.00250.008766.5381117.894156.4079
30.85960.1229-0.26080.34010.03270.9010.04250.34510.1023-0.0749-0.02370.0758-0.1324-0.302-0.01890.01260.092-0.01950.12540.01830.045960.0807110.51523.9959
40.09030.1363-0.07570.30810.21631.1347-0.07090.01750.0748-0.02350.0123-0.03450.1246-0.15650.0586-0.0274-0.03380.00540.0104-0.0165-0.014955.164473.090923.4475
50.0252-0.0783-0.14450.33370.3251.0001-0.0112-0.03430.0777-0.0123-0.0096-0.03040.09120.10510.02080.01410.02380.0119-0.0550.0268-0.03489.40956.479126.6516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2564 - 259
2X-RAY DIFFRACTION2BB1 - 2564 - 259
3X-RAY DIFFRACTION3CC1 - 2564 - 259
4X-RAY DIFFRACTION4DD1 - 2564 - 259
5X-RAY DIFFRACTION5EE1 - 2564 - 259

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