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- PDB-9bbo: Proline utilization A complexed with the product L-glutamate in t... -

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Basic information

Entry
Database: PDB / ID: 9bbo
TitleProline utilization A complexed with the product L-glutamate in the aldehyde dehydrogenase active site
ComponentsTrifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / GAMMA-L-GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsTanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Visualization of covalent intermediates and conformational states of proline utilization A by X-ray crystallography and molecular dynamics simulations.
Authors: Buckley, D.P. / Becker, D.F. / Tanner, J.J.
History
DepositionApr 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 10, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
B: Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,06018
Polymers263,9232
Non-polymers3,13616
Water35,7061982
1
A: Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5259
Polymers131,9621
Non-polymers1,5638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5359
Polymers131,9621
Non-polymers1,5738
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.377, 102.435, 127.598
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase


Mass: 131961.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: putA, GHK55_27665 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA90VXT3

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Non-polymers , 6 types, 1998 molecules

#2: Chemical ChemComp-GGL / GAMMA-L-GLUTAMIC ACID / L-GLUTAMIC ACID


Type: L-gamma-peptide, C-delta linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1982 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES AT PH 7.5, 0.1 M AMMONIUM SULFATE, 0.1 M LITHIUM SULFATE MONOHYDRATE, 50 MM MGCL2, AND 25% (W/V) PEG 3350; crystal soaked in 325 mM L-glutamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.5→102.43 Å / Num. obs: 386803 / % possible obs: 97.2 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 17.5 / Num. measured all: 2347695
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.783 / Num. measured all: 74652 / Num. unique obs: 19361 / CC1/2: 0.627 / Rpim(I) all: 0.459 / Rrim(I) all: 0.911 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→51.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 19610 5.07 %
Rwork0.1694 --
obs0.1705 386747 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→51.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18143 0 198 1982 20323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618902
X-RAY DIFFRACTIONf_angle_d0.8525775
X-RAY DIFFRACTIONf_dihedral_angle_d13.6177019
X-RAY DIFFRACTIONf_chiral_restr0.053004
X-RAY DIFFRACTIONf_plane_restr0.0083367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29016440.270311910X-RAY DIFFRACTION95
1.52-1.540.28446680.256311915X-RAY DIFFRACTION95
1.54-1.550.26226680.237511962X-RAY DIFFRACTION95
1.55-1.570.24456130.22511995X-RAY DIFFRACTION95
1.57-1.590.24766520.219411951X-RAY DIFFRACTION95
1.59-1.620.22846390.205912073X-RAY DIFFRACTION96
1.62-1.640.22366330.197612061X-RAY DIFFRACTION96
1.64-1.660.21246350.192912006X-RAY DIFFRACTION96
1.66-1.690.22676260.188712182X-RAY DIFFRACTION96
1.69-1.720.20836150.186812068X-RAY DIFFRACTION96
1.72-1.750.21356210.181412137X-RAY DIFFRACTION96
1.75-1.780.22186270.188712159X-RAY DIFFRACTION96
1.78-1.810.21586350.185512151X-RAY DIFFRACTION97
1.81-1.850.21466530.189212197X-RAY DIFFRACTION97
1.85-1.890.20896700.187512142X-RAY DIFFRACTION97
1.89-1.930.20647040.178512197X-RAY DIFFRACTION97
1.93-1.980.20796480.173612214X-RAY DIFFRACTION97
1.98-2.040.19956590.169512199X-RAY DIFFRACTION97
2.04-2.10.20546740.173112357X-RAY DIFFRACTION98
2.1-2.160.19376450.169812286X-RAY DIFFRACTION98
2.16-2.240.19776530.164412398X-RAY DIFFRACTION98
2.24-2.330.1876610.166512340X-RAY DIFFRACTION98
2.33-2.440.19056650.16812369X-RAY DIFFRACTION98
2.44-2.570.21036680.17512435X-RAY DIFFRACTION98
2.57-2.730.18967070.175812384X-RAY DIFFRACTION98
2.73-2.940.19826830.179212485X-RAY DIFFRACTION99
2.94-3.230.19376450.173612511X-RAY DIFFRACTION99
3.23-3.70.17766410.159812605X-RAY DIFFRACTION99
3.7-4.660.13846470.130812688X-RAY DIFFRACTION99
4.66-51.770.15077110.139812760X-RAY DIFFRACTION99
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)
10.6666-0.040.20980.1451-0.02830.2358-0.0397-0.0990.00020.05270.04540.032-0.0227-0.0387-0.00580.1280.01840.02190.08520.01650.1032-25.863766.076893.8122
20.2052-0.00560.07490.3191-0.02560.49490.0213-0.025-0.01540.07220.0212-0.01950.0857-0.0355-0.03780.0940.0081-0.01140.1075-0.01650.10385.463731.229692.7031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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