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- PDB-4nm9: Crystal structure of the resting state of proline utilization A (... -

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Basic information

Entry
Database: PDB / ID: 4nm9
TitleCrystal structure of the resting state of proline utilization A (PutA) from Geobacter sulfurreducens PCA
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 / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 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

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)227,58626
Polymers224,6492
Non-polymers2,93724
Water21,7621208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-32 kcal/mol
Surface area66850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.246, 151.209, 175.126
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / 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: 56.18 %
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-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012
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: 1.898→49.052 Å / Num. all: 197435 / Num. obs: 197435 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 23.93 Å2 / Rsym value: 0.076 / 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
1.898-24.50.5361.4129086285280.53699.1
2-2.124.50.3532.2124174272940.35399.8
2.12-2.274.50.2383.2113959254650.23899
2.27-2.454.60.1714.4111001238890.17199.7
2.45-2.684.40.125696049217580.12598.7
2.68-34.70.0888.494172200080.08899.8
3-3.474.50.05313.778428174590.05398.5
3.47-4.244.70.0332170573149930.03399.4
4.24-64.50.02823.951893115150.02897.9
6-49.0524.50.02327.52924965260.02397.5

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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: 1.898→49.052 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.883 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 9936 5.04 %RANDOM
Rwork0.1626 ---
obs0.1641 197290 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.41 Å2 / Biso mean: 21.4845 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: LAST / Resolution: 1.898→49.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15103 0 194 1208 16505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715642
X-RAY DIFFRACTIONf_angle_d1.02921194
X-RAY DIFFRACTIONf_chiral_restr0.0692316
X-RAY DIFFRACTIONf_plane_restr0.0042755
X-RAY DIFFRACTIONf_dihedral_angle_d14.1245751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.898-1.96580.27439760.2423184301940699
1.9658-2.04460.253110290.21011867819707100
2.0446-2.13760.24269490.18951873019679100
2.1376-2.25030.214910010.1723185471954899
2.2503-2.39130.2189320.16291881219744100
2.3913-2.57590.20719860.161187911977799
2.5759-2.83510.189410040.1547186351963999
2.8351-3.24530.200510350.16941885119886100
3.2453-4.08840.172710240.1523187431976798
4.0884-49.06890.152410000.1408191372013798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6268-0.0771-0.11250.11040.07860.4154-0.00880.09160.0601-0.01140.0054-0.0295-0.04310.0641-0.00070.1316-0.0107-0.02460.11710.00590.108451.153-5.35261.1265
20.1055-0.0958-0.06390.4720.24320.4748-0.01180.01230.040.01360.008-0.0076-0.04650.01230.00250.0919-0.0126-0.00990.11760.00990.104312.400824.732738.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 0:1003A0 - 1003
2X-RAY DIFFRACTION2chain B and resseq 3:1003B3 - 1003

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