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- PDB-4nmd: Crystal structure of proline utilization A (PutA) from Geobacter ... -

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Basic information

Entry
Database: PDB / ID: 4nmd
TitleCrystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA reduced with dithionite
ComponentsProline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / flavoenzyme / Rossmann fold / aldehyde dehydrogenase / flavin adenine dinucleotide / nicotinamide adenine dinucleotide / proline catabolism / substrate channeling / bifunctional enzyme
Function / homology
Function and homology information


proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding
Similarity search - Function
Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsSingh, H. / Tanner, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
Authors: Singh, H. / Arentson, B.W. / Becker, D.F. / Tanner, J.J.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 20, 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 / 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_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: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,09318
Polymers224,6492
Non-polymers2,44416
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint7 kcal/mol
Surface area65400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.173, 151.359, 175.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDimer in solution state verified by SAXS.

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Components

#1: Protein Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase / Proline utilization A / PutA


Mass: 112324.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: Q746X3, EC: 1.5.99.8, EC: 1.5.1.12, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 23% PEG400, 0.1 M MES, pH 5.8, N-terminal His Tag cleaved with TEV protease prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.979→49.094 Å / Num. all: 172814 / Num. obs: 172814 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.086 / Rsym value: 0.065 / Net I/av σ(I): 11.375 / Net I/σ(I): 14.6 / Num. measured all: 651971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.98-2.093.80.6051.394509250620.3690.7480.6052.498.4
2.09-2.213.60.3921.984675236610.2460.4910.3923.597.8
2.21-2.373.90.253388317225430.1540.3140.2535.599.3
2.37-2.563.90.1724.481143210070.1070.2180.1727.699.1
2.56-2.83.70.1116.869839190400.0710.1430.11110.997.7
2.8-3.133.90.07210.667994174460.0480.0960.07216.298.6
3.13-3.613.80.04317.659557154720.0270.0560.04326.398.8
3.61-4.433.60.02725.946173128340.0180.0360.02737.696.6
4.43-6.263.90.02330.539394101870.0140.0290.02343.497.9
6.26-49.0943.70.01734.62037055620.0110.0220.01750.894.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NMC

4nmc


Resolution: 1.979→49.094 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.873 / SU ML: 0.2 / σ(F): 0 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 8669 5.02 %TEST SET FOR NPPG-REDUCED STRUCTURE OF THE SAME ENZYME
Rwork0.1652 ---
obs0.1669 172690 97.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.17 Å2 / Biso mean: 24.604 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: LAST / Resolution: 1.979→49.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15114 0 162 919 16195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715637
X-RAY DIFFRACTIONf_angle_d1.03421205
X-RAY DIFFRACTIONf_chiral_restr0.0682318
X-RAY DIFFRACTIONf_plane_restr0.0042763
X-RAY DIFFRACTIONf_dihedral_angle_d14.2155740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.979-2.00190.27562930.23555313560697
2.0019-2.02540.29642910.23655502579399
2.0254-2.05010.26432970.23445428572599
2.0501-2.07610.27212680.22885469573798
2.0761-2.10340.25562720.2225463573598
2.1034-2.13220.26712910.20425409570098
2.1322-2.16270.25232960.19915415571198
2.1627-2.1950.24032800.19375303558396
2.195-2.22930.23242900.18495488577899
2.2293-2.26580.23822980.17855491578999
2.2658-2.30490.22522660.17925486575299
2.3049-2.34680.2462600.17255526578699
2.3468-2.39190.23922860.16665529581599
2.3919-2.44080.22562950.1735550584599
2.4408-2.49380.24422900.17055457574799
2.4938-2.55180.21192900.16775488577899
2.5518-2.61570.20042940.165474576899
2.6157-2.68640.2032880.16195424571298
2.6864-2.76540.22012980.17165414571297
2.7654-2.85470.23022720.17955349562196
2.8547-2.95670.22323020.17815490579299
2.9567-3.0750.19543060.17535516582298
3.075-3.2150.2063050.16965486579199
3.215-3.38440.2042740.16965568584299
3.3844-3.59640.18963120.16155479579198
3.5964-3.8740.16462900.14385456574697
3.874-4.26360.15052840.13635358564295
4.2636-4.88010.14232810.12395584586598
4.8801-6.14660.16463010.14965546584797
6.1466-49.10880.16192990.15265560585993

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