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- PDB-1yqg: Crystal structure of a pyrroline-5-carboxylate reductase from nei... -

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Basic information

Entry
Database: PDB / ID: 1yqg
TitleCrystal structure of a pyrroline-5-carboxylate reductase from neisseria meningitides mc58
Componentspyrroline-5-carboxylate reductase
KeywordsOXIDOREDUCTASE / PYRROLINE-5-CARBOXYLATE REDUCTASE / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
Pyrroline-5-carboxylate reductase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsChang, C. / Joachimiak, A. / Li, H. / Collart, F. / 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
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2005ID: 1XC2
Revision 1.0Feb 8, 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 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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_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: pyrroline-5-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8962
Polymers28,7991
Non-polymers961
Water4,468248
1
A: pyrroline-5-carboxylate reductase
hetero molecules

A: pyrroline-5-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7914
Polymers57,5992
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8790 Å2
ΔGint-116 kcal/mol
Surface area21880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.526, 49.845, 65.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

DetailsThe second part of the biological assembly is generated by operation of 1-x, 1-y, Z

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Components

#1: Protein pyrroline-5-carboxylate reductase


Mass: 28799.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K1N1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AMMONIUM SULFATE, HEPES, PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97984, 0.97970
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 23, 2004
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979841
20.97971
ReflectionResolution: 1.61→50 Å / Num. all: 38574 / Num. obs: 26616 / % possible obs: 69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.66
Reflection shellResolution: 1.61→1.67 Å / % possible all: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.742 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24059 1205 5.1 %RANDOM
Rwork0.19495 ---
all0.19727 22585 --
obs0.19727 22303 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.446 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 5 248 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9692703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06823.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05615355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0311520
X-RAY DIFFRACTIONr_chiral_restr0.1090.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21002
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21424
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0921.51326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58422044
X-RAY DIFFRACTIONr_scbond_it3.8813763
X-RAY DIFFRACTIONr_scangle_it5.2764.5659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 80 -
Rwork0.258 1449 -
obs--88.43 %
Refinement TLS params.Method: refined / Origin x: 29.29 Å / Origin y: 31.383 Å / Origin z: 15.071 Å
111213212223313233
T-0.0465 Å20.0213 Å2-0.0338 Å2--0.0788 Å20.0289 Å2---0.1388 Å2
L1.8334 °2-1.1992 °2-0.6702 °2-1.4158 °20.4983 °2--1.5468 °2
S0.1052 Å °0.0914 Å °-0.0979 Å °-0.154 Å °-0.0472 Å °0.1431 Å °-0.1772 Å °-0.2228 Å °-0.0579 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1061 - 106
2X-RAY DIFFRACTION1AA107 - 151107 - 151
3X-RAY DIFFRACTION1AA152 - 186152 - 186
4X-RAY DIFFRACTION1AA187 - 211187 - 211
5X-RAY DIFFRACTION1AA212 - 224212 - 224
6X-RAY DIFFRACTION1AA225 - 263225 - 263

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