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- PDB-3tri: Structure of a pyrroline-5-carboxylate reductase (proC) from Coxi... -

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Basic information

Entry
Database: PDB / ID: 3tri
TitleStructure of a pyrroline-5-carboxylate reductase (proC) from Coxiella burnetii
ComponentsPyrroline-5-carboxylate reductase
KeywordsOXIDOREDUCTASE / Amino acid biosynthesis
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Pyrroline-5-carboxylate reductase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.5 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 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
B: Pyrroline-5-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4279
Polymers61,5242
Non-polymers1,9027
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-141 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.411, 75.411, 189.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pyrroline-5-carboxylate reductase


Mass: 30762.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_2090, proC / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83A21, pyrroline-5-carboxylate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M glycine, 1.2M sodium dihydrogen phosphate, 0.8M dipotassium hydrogen phosphate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21008 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.087 / Χ2: 0.69 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.443.30.69423250.523198.4
2.44-2.493.90.60323070.5199.5
2.49-2.534.10.55723330.482199.8
2.53-2.594.40.48823990.4891100
2.59-2.644.50.42823540.5011100
2.64-2.74.50.39723310.5161100
2.7-2.774.50.32523680.5011100
2.77-2.854.50.27723170.511100
2.85-2.934.50.23823580.5241100
2.93-3.024.50.18923830.5381100
3.02-3.134.50.15223370.5731100
3.13-3.264.50.12523320.6181100
3.26-3.414.50.10423380.7061100
3.41-3.584.40.07523800.7961100
3.58-3.814.40.06523230.9421100
3.81-4.14.40.05323720.9711100
4.1-4.524.40.04623581.0281100
4.52-5.174.40.04223401.0131100
5.17-6.514.30.04923571.011100
6.51-504.20.02823571.027199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→37.705 Å / Occupancy max: 1 / Occupancy min: 0.54 / FOM work R set: 0.8301 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1085 5.16 %RANDOM
Rwork0.182 ---
all0.1849 22097 --
obs0.1849 21008 99.98 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.27 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 149.64 Å2 / Biso mean: 42.5074 Å2 / Biso min: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.2574 Å2-0 Å20 Å2
2--0.2574 Å20 Å2
3----0.5148 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 117 109 4323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034259
X-RAY DIFFRACTIONf_angle_d0.7985785
X-RAY DIFFRACTIONf_chiral_restr0.047707
X-RAY DIFFRACTIONf_plane_restr0.002723
X-RAY DIFFRACTIONf_dihedral_angle_d15.941597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.61380.29771260.212724942620
2.6138-2.75160.2931530.203824472600
2.7516-2.92390.2631050.202925312636
2.9239-3.14960.29631310.190324982629
3.1496-3.46630.24391430.192724562599
3.4663-3.96750.21381320.163325242656
3.9675-4.99670.18581460.147924882634
4.9967-37.70980.23941490.201224852634

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