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

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Basic information

Entry
Database: PDB / ID: 4nme
TitleCrystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine
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 / mechanism-based inactivation
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
Chem-P5F / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)227,44020
Polymers224,6492
Non-polymers2,79018
Water17,132951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint28 kcal/mol
Surface area65970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.235, 151.177, 175.180
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-P5F / N-propargylglycine-modified flavin adenine dinucleotide


Mass: 898.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H40N10O17P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 951 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 25-33% PEG550 MME, 0.05-0.2 M Bis-Tris, pH 6.4 - 6.5, 0.05 mM 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: Jul 2, 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: 2.088→175.18 Å / Num. all: 149802 / Num. obs: 149802 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.35 Å2 / Rsym value: 0.099 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.088-2.24.20.5311.490118214380.53198.6
2.2-2.334.20.4251.785250204550.42599.5
2.33-2.54.40.2942.684928193900.294100
2.5-2.74.50.2143.580479180430.21499.9
2.7-2.954.50.1574.875264166320.157100
2.95-3.34.50.095868322151520.095100
3.3-3.814.40.05314.159097133560.05399.8
3.81-4.674.40.03420.949561113320.03499.9
4.67-6.64.50.03222.34010489290.03299.9
6.6-175.184.30.02426.52159950750.02499.5

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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: 2.088→87.59 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8772 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 7525 5.03 %RANDOM
Rwork0.1691 ---
obs0.1711 149635 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.07 Å2 / Biso mean: 24.6641 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: LAST / Resolution: 2.088→87.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15118 0 176 951 16245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715643
X-RAY DIFFRACTIONf_angle_d1.02921188
X-RAY DIFFRACTIONf_chiral_restr0.0682309
X-RAY DIFFRACTIONf_plane_restr0.0052758
X-RAY DIFFRACTIONf_dihedral_angle_d13.9445765
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 (%)
2.088-2.11150.30712410.24824435467694
2.1115-2.13640.28152410.22247054946100
2.1364-2.16240.25912520.212747234975100
2.1624-2.18980.26182480.210146734921100
2.1898-2.21860.26912390.226947224961100
2.2186-2.2490.30152610.2614573483498
2.249-2.28120.28252380.21584686492499
2.2812-2.31520.23672200.191347684988100
2.3152-2.35140.27052290.182846904919100
2.3514-2.38990.24942460.176647224968100
2.3899-2.43120.23322660.18147304996100
2.4312-2.47540.24932390.182547214960100
2.4754-2.5230.2342520.177747224974100
2.523-2.57450.23092300.178647394969100
2.5745-2.63050.21512600.167647304990100
2.6305-2.69170.20862580.162247134971100
2.6917-2.7590.21752570.168346984955100
2.759-2.83360.22082500.173347494999100
2.8336-2.9170.21312670.172747244991100
2.917-3.01110.23212550.176647354990100
3.0111-3.11870.21222650.177447575022100
3.1187-3.24360.23732510.179847464997100
3.2436-3.39130.20412310.168947875018100
3.3913-3.570.20272650.165447755040100
3.57-3.79370.17832680.150347425010100
3.7937-4.08660.16442690.142147605029100
4.0866-4.49790.15632430.130848235066100
4.4979-5.14870.14462360.128248475083100
5.1487-6.48650.19032750.163548745149100
6.4865-87.66710.1652730.15045041531499

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