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- PDB-6vh5: Crystal structure of prephenate dehydratase from brucella meliten... -

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Basic information

Entry
Database: PDB / ID: 6vh5
TitleCrystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine
ComponentsPrephenate dehydratase:Amino acid-binding ACT
KeywordsHYDROLASE / SSGCID / Prephenate dehydratase / Amino acid-binding ACT / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / chorismate mutase activity / L-phenylalanine biosynthetic process
Similarity search - Function
Prephenate dehydratase signature 1. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain profile. / ACT domain / Periplasmic binding protein-like II ...Prephenate dehydratase signature 1. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain profile. / ACT domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Prephenate dehydratase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of prephenate dehydratase from Brucella melitensis biovar abortus 2308 in complex with phenylalanine
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Bullen, J.C. / Sankaran, B. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prephenate dehydratase:Amino acid-binding ACT
B: Prephenate dehydratase:Amino acid-binding ACT
C: Prephenate dehydratase:Amino acid-binding ACT
D: Prephenate dehydratase:Amino acid-binding ACT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,56014
Polymers136,5274
Non-polymers1,03310
Water3,027168
1
A: Prephenate dehydratase:Amino acid-binding ACT
C: Prephenate dehydratase:Amino acid-binding ACT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7186
Polymers68,2642
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-16 kcal/mol
Surface area23380 Å2
MethodPISA
2
B: Prephenate dehydratase:Amino acid-binding ACT
D: Prephenate dehydratase:Amino acid-binding ACT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8428
Polymers68,2642
Non-polymers5796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-10 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.950, 61.250, 120.050
Angle α, β, γ (deg.)90.000, 112.950, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 through 2 and (name N...
21(chain B and (resid 1 through 105 or (resid 106...
31(chain C and (resid 1 through 42 or (resid 43...
41(chain D and (resid 1 through 42 or (resid 43...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and ((resid 1 through 2 and (name N...AA1 - 222 - 23
12SERSERGLYGLY(chain A and ((resid 1 through 2 and (name N...AA0 - 28021 - 301
13SERSERGLYGLY(chain A and ((resid 1 through 2 and (name N...AA0 - 28021 - 301
14SERSERGLYGLY(chain A and ((resid 1 through 2 and (name N...AA0 - 28021 - 301
15SERSERGLYGLY(chain A and ((resid 1 through 2 and (name N...AA0 - 28021 - 301
21METMETHISHIS(chain B and (resid 1 through 105 or (resid 106...BB1 - 10522 - 126
22ILEILEILEILE(chain B and (resid 1 through 105 or (resid 106...BB106127
23METMETGLYGLY(chain B and (resid 1 through 105 or (resid 106...BB1 - 28022 - 301
31METMETVALVAL(chain C and (resid 1 through 42 or (resid 43...CC1 - 4222 - 63
32GLUGLUGLUGLU(chain C and (resid 1 through 42 or (resid 43...CC4364
33METMETARGARG(chain C and (resid 1 through 42 or (resid 43...CC1 - 27922 - 300
34METMETARGARG(chain C and (resid 1 through 42 or (resid 43...CC1 - 27922 - 300
35METMETARGARG(chain C and (resid 1 through 42 or (resid 43...CC1 - 27922 - 300
36METMETARGARG(chain C and (resid 1 through 42 or (resid 43...CC1 - 27922 - 300
41METMETVALVAL(chain D and (resid 1 through 42 or (resid 43...DD1 - 4222 - 63
42GLUGLUGLUGLU(chain D and (resid 1 through 42 or (resid 43...DD4364
43PROPROARGARG(chain D and (resid 1 through 42 or (resid 43...DD-2 - 27919 - 300
44PROPROARGARG(chain D and (resid 1 through 42 or (resid 43...DD-2 - 27919 - 300
45PROPROARGARG(chain D and (resid 1 through 42 or (resid 43...DD-2 - 27919 - 300
46PROPROARGARG(chain D and (resid 1 through 42 or (resid 43...DD-2 - 27919 - 300

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Components

#1: Protein
Prephenate dehydratase:Amino acid-binding ACT


Mass: 34131.777 Da / Num. of mol.: 4 / Fragment: BrabA.00146.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: pheA, BAB1_0034 / Plasmid: BrabA.00146.a.A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q2YPM5, prephenate dehydratase
#2: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents PACT screen, condition E12:200mM sodium malonate, dibasic, 20% PEG 3350: BrabA.00146.a.A1.PW25617 at 28.9mg/ml: cryo: 20% EG: tray: 216998 e6, puck gej7-16.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.4→41.41 Å / Num. obs: 59038 / % possible obs: 98.4 % / Redundancy: 4.465 % / Biso Wilson estimate: 60.259 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.065 / Χ2: 1.062 / Net I/σ(I): 12.82 / Num. measured all: 263583 / Scaling rejects: 1290
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.464.6090.5462.3320152440243720.9660.61999.3
2.46-2.534.6030.4882.5919583427942540.9690.55499.4
2.53-2.64.610.393.2719195418241640.9720.44399.6
2.6-2.684.6020.2924.0418533405540270.9840.33299.3
2.68-2.774.5920.235.1417903392638990.9880.26299.3
2.77-2.874.5690.1816.3617331382437930.9910.20799.2
2.87-2.984.5750.1557.4316520364236110.9930.17799.1
2.98-3.14.540.1239.1115991355235220.9940.1499.2
3.1-3.244.5120.09911.0115322343233960.9950.11399
3.24-3.394.4630.07513.8614327324532100.9970.08698.9
3.39-3.584.4010.06216.4713273308730160.9980.07297.7
3.58-3.794.3290.05420.0112484293828840.9980.06298.2
3.79-4.064.2670.04622.4111428278026780.9980.05396.3
4.06-4.384.1790.0425.5910218255324450.9980.04695.8
4.38-4.84.190.03827.819533237022750.9980.04496
4.8-5.374.2060.03729.198867216521080.9980.04297.4
5.37-6.24.1790.03628.457828191318730.9990.04197.9
6.2-7.594.3010.03230.396895164316030.9990.03697.6
7.59-10.734.3720.02733.475412126812380.9990.03197.6
10.73-41.414.1610.02633.5127887416700.9990.02990.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A

Resolution: 2.4→41.41 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1873 3.18 %0
Rwork0.2069 ---
obs0.2083 58845 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.77 Å2 / Biso mean: 70.4797 Å2 / Biso min: 31.27 Å2
Refinement stepCycle: final / Resolution: 2.4→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8438 0 72 168 8678
Biso mean--59.66 61.24 -
Num. residues----1122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068682
X-RAY DIFFRACTIONf_angle_d0.78311805
X-RAY DIFFRACTIONf_chiral_restr0.0531348
X-RAY DIFFRACTIONf_plane_restr0.0061564
X-RAY DIFFRACTIONf_dihedral_angle_d20.0933055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4980X-RAY DIFFRACTION8.223TORSIONAL
12B4980X-RAY DIFFRACTION8.223TORSIONAL
13C4980X-RAY DIFFRACTION8.223TORSIONAL
14D4980X-RAY DIFFRACTION8.223TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.45131430.37034350449399
2.46-2.540.44491790.35614353453299
2.54-2.620.40321310.31644365449699
2.62-2.710.35161360.27684403453999
2.71-2.820.37361400.2694395453599
2.82-2.950.33521360.26794406454299
2.95-3.110.3521530.26544376452999
3.11-3.30.30511520.25074386453899
3.3-3.550.27781560.23594364452098
3.55-3.910.23291480.20184373452198
3.91-4.480.16371230.16094296441996
4.48-5.640.17341390.14824403454297
5.64-41.410.20161370.16614502463997
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)
122.00071.99911.99921.99962.0005-0.14610.33960.2744-0.36270.11490.0783-0.00520.0587-0.33140.47340.1683-0.14150.5397-0.10620.497787.67536.85230.999
26.5195-0.20250.27793.9054-0.1585.01460.0828-0.31330.4358-0.3311-0.331-0.0693-0.5935-1.0872-0.05290.4980.19920.05280.4515-0.00320.456539.22261.55888.62
36.2821-0.07890.65112.8176-0.66825.98040.17810.5308-0.355-0.1837-0.11780.1656-0.015-0.2395-0.04750.49850.11830.01670.5962-0.00190.449143.58253.59984.837
43.3485-0.577-2.66680.9656-0.27444.37230.045-0.27030.13960.08910.096-0.0216-0.3235-0.0363-0.09140.5390.155-0.01690.7606-0.05320.432142.07257.367102.915
53.9713-1.45520.3643.9074-0.91092.64510.27130.4084-0.1166-0.1773-0.27550.2892-0.1088-0.03930.01640.36620.08370.00520.5218-0.03990.326264.47148.8979.036
65.97916.12291.3366.48480.08798.00350.0148-0.548-0.6960.4692-0.04030.36270.13780.04870.05980.5356-0.04460.07280.37660.0120.506968.4750.42988.839
75.10861.4323-0.83353.39480.90095.17860.16230.30550.0276-0.42340.01390.4155-0.5126-1.0754-0.13590.5160.2054-0.03430.71180.09420.544360.27460.22431.72
84.86170.5529-2.32633.76580.9141.83050.01080.5277-0.8291-0.40920.0120.27780.1102-0.105-0.00670.48950.1185-0.00310.7802-0.02840.494268.77151.75531.192
96.3409-0.288-3.32140.8233-0.68584.66550.0598-0.39780.24810.08310.11490.23-0.427-0.2424-0.14970.52770.15530.01750.63220.01840.455860.23459.27551.161
100.5194-0.90660.61761.6919-0.56975.69930.56710.68190.02310.6462-0.0584-0.2397-1.0438-0.909-0.45580.82370.1432-0.00380.69220.15010.594580.09964.52620.813
113.2526-1.34730.00173.5079-0.36411.84620.24260.613-0.1433-0.3471-0.26710.0984-0.143-0.02480.02760.44790.0688-0.00560.627-0.02380.327585.83748.93325.858
126.82186.0868-1.65616.85941.59676.9996-0.1613-0.1479-0.18930.2438-0.0884-0.1143-0.26310.25480.03570.54230.00960.01340.62360.04980.419789.62651.25735.438
134.7153-0.1617-1.15024.5922-0.40725.3604-0.0653-0.2729-0.49480.20190.0785-0.00230.2535-0.7103-0.07060.3619-0.08240.01790.63430.0590.49448.6230.538101.849
145.76490.80753.0427-0.19440.61372.8666-0.30730.4065-0.3231-0.22590.05790.2226-0.0303-0.4150.23660.6465-0.2256-0.09420.87610.02370.773433.46230.27888.544
153.54680.026-0.26853.3262-2.03364.13440.0111-0.3579-0.4690.1339-0.0437-0.03430.23530.20840.03230.3337-0.02290.01060.44560.03990.381169.57336.24393.925
162-2.54541.99999.67132.00051.99950.09580.64130.538-0.31260.29680.14740.1335-0.1094-0.49870.42350.092-0.0350.66510.02680.549166.63336.51283.043
173.86890.4835-1.01023.9034-0.73794.4979-0.17170.4422-0.39370.03260.4940.40360.2566-0.8539-0.34290.3441-0.05550.02670.51240.04970.571769.35332.63350.048
185.2618-0.64642.6534-0.52691.11471.7255-0.39351.1336-0.1858-0.16680.10870.0058-0.33890.21520.28720.6947-0.3424-0.08770.85060.11020.75154.54531.07634.998
193.49440.4695-0.12483.3106-0.94572.73180.0698-0.1132-0.45860.0391-0.0928-0.11180.07090.11180.02280.3004-0.0529-0.01580.3950.0030.364790.69237.58841.757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 301:301 )D301
2X-RAY DIFFRACTION2( CHAIN A AND RESID 0:23 )A0 - 23
3X-RAY DIFFRACTION3( CHAIN A AND RESID 24:74 )A24 - 74
4X-RAY DIFFRACTION4( CHAIN A AND RESID 75:193 )A75 - 193
5X-RAY DIFFRACTION5( CHAIN A AND RESID 194:280 )A194 - 280
6X-RAY DIFFRACTION6( CHAIN A AND RESID 301:301 )A301
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:44 )B1 - 44
8X-RAY DIFFRACTION8( CHAIN B AND RESID 45:74 )B45 - 74
9X-RAY DIFFRACTION9( CHAIN B AND RESID 75:179 )B75 - 179
10X-RAY DIFFRACTION10( CHAIN B AND RESID 180:193 )B180 - 193
11X-RAY DIFFRACTION11( CHAIN B AND RESID 194:280 )B194 - 280
12X-RAY DIFFRACTION12( CHAIN B AND RESID 301:301 )B301
13X-RAY DIFFRACTION13( CHAIN C AND RESID 1:74 )C1 - 74
14X-RAY DIFFRACTION14( CHAIN C AND RESID 75:179 )C75 - 179
15X-RAY DIFFRACTION15( CHAIN C AND RESID 180:279 )C180 - 279
16X-RAY DIFFRACTION16( CHAIN C AND RESID 301:301 )C301
17X-RAY DIFFRACTION17( CHAIN D AND RESID -2:74 )D-2 - 74
18X-RAY DIFFRACTION18( CHAIN D AND RESID 75:179 )D75 - 179
19X-RAY DIFFRACTION19( CHAIN D AND RESID 180:279 )D180 - 279

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