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

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Basic information

Entry
Database: PDB / ID: 4nmb
TitleCrystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA in complex with L-lactate
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
(2S)-2-HYDROXYPROPANOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsSingh, H. / Almo, S.C. / 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
SupersessionFeb 19, 2014ID: 4F9I
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)226,7918
Polymers224,6492
Non-polymers2,1426
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-38 kcal/mol
Surface area64640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.648, 152.063, 175.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 23% PEG400, 0.1 M MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.198→114.821 Å / Num. all: 129595 / Num. obs: 129595 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.11 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.198-2.323.80.7160.970119182420.71697
2.32-2.464.30.3971.976433178420.39799.9
2.46-2.634.40.3042.573827167300.30499.9
2.63-2.844.50.2133.670738156600.213100
2.84-3.114.60.152565729144410.152100
3.11-3.484.50.098.559243130720.0999.9
3.48-4.014.50.05413.951912116190.05499.9
4.01-4.924.40.03719.84338898630.03799.9
4.92-6.954.40.03520.43379877290.03599.9
6.95-175.1334.20.02324.71847743970.02399

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NMC

4nmc


Resolution: 2.198→114.821 Å / Occupancy max: 1 / Occupancy min: 0.94 / FOM work R set: 0.8559 / SU ML: 0.26 / σ(F): 0 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 6511 5.03 %RANDOM
Rwork0.1798 ---
obs0.1819 129430 99.36 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.71 Å2 / Biso mean: 27.6985 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: LAST / Resolution: 2.198→114.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15068 0 142 629 15839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815560
X-RAY DIFFRACTIONf_angle_d1.04721125
X-RAY DIFFRACTIONf_chiral_restr0.0712311
X-RAY DIFFRACTIONf_plane_restr0.0042750
X-RAY DIFFRACTIONf_dihedral_angle_d14.9045705
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 (%)
2.198-2.22310.39281990.3273891409094
2.2231-2.24920.39342110.35663742395393
2.2492-2.27670.38032070.32564043425098
2.2767-2.30550.27992020.218440524254100
2.3055-2.33580.28741910.202841204311100
2.3358-2.36780.28392080.19640514259100
2.3678-2.40170.22292120.188941104322100
2.4017-2.43750.25462270.200840524279100
2.4375-2.47560.29332080.194840694277100
2.4756-2.51620.25652260.194640754301100
2.5162-2.55960.23232080.193441134321100
2.5596-2.60610.24022090.180540854294100
2.6061-2.65630.23022170.179141004317100
2.6563-2.71050.23472170.178240894306100
2.7105-2.76940.23962340.193940744308100
2.7694-2.83380.24412230.197340964319100
2.8338-2.90470.26232110.204441234334100
2.9047-2.98330.27272170.202641394356100
2.9833-3.0710.24382280.204340584286100
3.071-3.17020.2612410.195140994340100
3.1702-3.28350.21782010.195141084309100
3.2835-3.4150.24082040.182341524356100
3.415-3.57040.20882310.175741084339100
3.5704-3.75860.18312320.159441284360100
3.7586-3.99420.15792230.143341604383100
3.9942-4.30260.15872220.131541184340100
4.3026-4.73550.15492160.123741924408100
4.7355-5.42080.15242140.132342014415100
5.4208-6.82950.19812410.164642254466100
6.8295-114.9780.16572310.15014346457798

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