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

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Basic information

Entry
Database: PDB / ID: 4nma
TitleCrystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA in complex with L-tetrahydro-2-furoic acid
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
FLAVIN-ADENINE DINUCLEOTIDE / TETRAHYDROFURAN-2-CARBOXYLIC ACID / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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 1.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)227,69426
Polymers224,6492
Non-polymers3,04524
Water13,295738
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15030 Å2
ΔGint13 kcal/mol
Surface area65780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.619, 151.743, 176.205
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-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 25-28% PEG550 MME, 0.05-0.15 M Bis-Tris, pH 6.3-6.5, 0.05 M calcium chloride, MICROBATCH, 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: Nov 25, 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: 2.101→47.529 Å / Num. all: 146947 / Num. obs: 146947 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.39 Å2 / Rsym value: 0.11 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.101-2.213.20.6051.166122208800.60596.7
2.21-2.353.20.4541.365299201720.45498.7
2.35-2.513.30.3122.263283190400.31299.1
2.51-2.713.40.2372.960538178230.23799.2
2.71-2.973.50.1793.857263164400.17999.7
2.97-3.323.40.1244.951137148300.12498.7
3.32-3.843.40.0786.843965130640.07898.4
3.84-4.73.30.05110.736434110620.05198
4.7-6.643.40.04114.62939487250.04198.7
6.64-47.5293.40.02819.81645249110.02897.7

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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: 2.101→46.141 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8602 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 7340 5.01 %FROM OPEN FORM STRUCTURE
Rwork0.1728 ---
obs0.1749 146604 98.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 23.5921 Å2 / Biso min: 8.77 Å2
Refinement stepCycle: LAST / Resolution: 2.101→46.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15129 0 202 738 16069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715663
X-RAY DIFFRACTIONf_angle_d1.0521210
X-RAY DIFFRACTIONf_chiral_restr0.0712316
X-RAY DIFFRACTIONf_plane_restr0.0042751
X-RAY DIFFRACTIONf_dihedral_angle_d14.25768
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 (%)
2.101-2.12460.33592010.26654230443190
2.1246-2.14960.28682440.23064604484898
2.1496-2.17580.27452140.22444633484798
2.1758-2.20340.28242610.22384578483998
2.2034-2.23240.26062420.22664592483498
2.2324-2.2630.30262560.24494571482798
2.263-2.29530.2822270.21094602482998
2.2953-2.32960.28372070.20084725493299
2.3296-2.3660.25872410.18944583482499
2.366-2.40470.24782410.17954619486099
2.4047-2.44620.23082470.18984684493199
2.4462-2.49070.26372450.19624634487999
2.4907-2.53860.26552470.19034634488199
2.5386-2.59040.21962270.18334662488998
2.5904-2.64670.21442550.1724653490899
2.6467-2.70830.23572480.1694659490799
2.7083-2.7760.22862620.17484630489299
2.776-2.8510.23172400.17384684492499
2.851-2.93490.22282660.184546774943100
2.9349-3.02960.25212550.18614722497799
3.0296-3.13790.24662590.17934634489399
3.1379-3.26350.21512420.1854616485897
3.2635-3.4120.18952270.17194675490298
3.412-3.59180.22742680.17024625489398
3.5918-3.81670.18822540.15664647490197
3.8167-4.11130.16242620.14244589485197
4.1113-4.52470.16132340.1344704493898
4.5247-5.17870.14732350.1334720495598
5.1787-6.52160.19922660.16464786505299
6.5216-46.15250.16032670.14734892515997

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