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- PDB-6u60: Crystal structure of prephenate dehydrogenase tyrA from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 6u60
TitleCrystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD and L-tyrosine
ComponentsPrephenate dehydrogenase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


prephenate dehydrogenase / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / L-phenylalanine biosynthetic process
Similarity search - Function
Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / ACT domain profile. / ACT domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / TYROSINE / Prephenate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShabalin, I.G. / Hou, J. / Kutner, J. / Grimshaw, S. / Christendat, D. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: Febs J. / Year: 2020
Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D.
History
DepositionAug 28, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionSep 11, 2019ID: 5USC
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prephenate dehydrogenase
B: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6317
Polymers85,4162
Non-polymers1,2165
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14370 Å2
ΔGint-105 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)106.850, 81.003, 83.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A14 - 378
2010B14 - 378

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Components

#1: Protein Prephenate dehydrogenase /


Mass: 42707.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: tyrA, GBAA_2954 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81P63, prephenate dehydrogenase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.2
Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M Potassium/Sodium phosphate pH=6.2, 0.2M Sodium chloride, 20% w/v PEG 1000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2015 / Details: Beryllium Lenses
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42991 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.027 / Rrim(I) all: 0.08 / Χ2: 0.965 / Net I/av σ(I): 27.8 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.71.3021.621370.6120.5341.4110.95499.3
2.14-2.187.20.97620660.7420.3831.0510.8799.3
2.18-2.227.80.82621040.8030.3110.8840.89699.6
2.22-2.268.20.73721380.8490.2680.7850.86399.7
2.26-2.318.30.65321170.8990.2370.6950.89699.8
2.31-2.378.40.53121100.9240.1920.5660.84499.9
2.37-2.428.40.43421390.9460.1570.4620.87699.9
2.42-2.498.50.36221320.9640.1310.3850.86499.9
2.49-2.568.60.3121030.9710.1120.330.891100
2.56-2.658.60.23921560.9820.0860.2550.87100
2.65-2.748.70.19521240.9890.070.2080.906100
2.74-2.858.90.15221420.9920.0540.1610.949100
2.85-2.9890.12121630.9950.0430.1280.979100
2.98-3.149.10.09321380.9950.0330.0990.998100
3.14-3.339.10.06821550.9970.0240.0721.018100
3.33-3.5990.05421560.9980.0190.0581.072100
3.59-3.9590.04821840.9980.0170.0511.229100
3.95-4.528.90.04521890.9970.0160.0481.367100
4.52-5.78.80.03622160.9990.0130.0380.993100
5.7-508.10.03423220.9980.0130.0370.86799.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
HKL-3000phasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GGG
Resolution: 2.1→36.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2086 / WRfactor Rwork: 0.1511 / FOM work R set: 0.8284 / SU B: 11.542 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2356 / SU Rfree: 0.1931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1975 4.9 %RANDOM
Rwork0.1605 ---
obs0.1634 38244 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.42 Å2 / Biso mean: 36.389 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0 Å2
2---0.2 Å20 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 2.1→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 80 370 6153
Biso mean--25.7 36.04 -
Num. residues----730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175509
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6317985
X-RAY DIFFRACTIONr_angle_other_deg1.3521.58212779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32223.287286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.419151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1631525
X-RAY DIFFRACTIONr_chiral_restr0.070.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021162
Refine LS restraints NCS

Ens-ID: 1 / Number: 10460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 95 -
Rwork0.234 1839 -
all-1934 -
obs--61.28 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.1624-2.25341.143.7095-1.54595.356-0.03250.57570.9529-0.31490.0160.1902-0.4431-0.3220.01650.22820.0566-0.14720.20080.11370.274750.45824.6079.696
24.7727-0.83050.30571.3887-0.89326.68730.0189-0.27970.5002-0.02120.06350.3758-0.6175-0.7517-0.08230.14560.0823-0.0420.2881-0.02180.238646.55220.73424.61
36.6050.7877-1.17322.1026-0.76634.6689-0.0437-0.09440.0339-0.05360.06670.23160.0715-0.1946-0.02310.13250.0264-0.05340.127-0.00640.044556.86512.5218.498
413.53410.08390.93229.44540.4591.51570.1877-0.0147-0.09610.2359-0.0077-0.1691-0.1177-0.0975-0.17990.07540.04110.0020.14650.00580.030775.50121.65632.76
53.07870.31210.08150.8595-0.0961.51040.0398-0.17630.09440.1096-0.00170.0159-0.2296-0.0788-0.03810.08680.0033-0.00820.1038-0.01260.011880.59423.12834.231
616.16955.367510.69335.14174.975813.06530.3911-0.4908-0.68680.1651-0.1984-0.24910.5951-0.5321-0.19270.1756-0.0015-0.01920.06510.00940.098687.2146.33628.612
73.36131.11870.43184.4333-0.17662.95450.0208-0.1001-0.3992-0.05260.0196-0.20710.3454-0.1369-0.04050.2045-0.0194-0.02680.0295-0.01130.077682.950.0987.173
83.46620.7022-0.19582.74991.35933.21210.03660.3183-0.2548-0.19720.1131-0.12740.08510.2899-0.14980.1585-0.00030.0090.1177-0.04170.1604116.33516.26315.099
99.2598-1.27452.59415.6746-6.28659.93720.2092-0.2773-0.24470.64860.1581-0.363-0.05850.8167-0.36740.13730.00990.01830.269-0.11770.1881126.35721.04525.072
103.74010.47690.57640.87290.23092.2254-0.00290.01610.188-0.07920.0746-0.0587-0.21580.2554-0.07170.1392-0.04120.0130.04930.00940.0797110.17327.68622.505
115.29552.64030.32163.00280.23081.2817-0.00610.1339-0.0656-0.0570.04820.14580.0636-0.1242-0.04220.08460.0035-0.00620.11980.01260.036287.24215.41329.855
122.8265-0.08990.08640.9546-0.24322.10720.086-0.27520.3970.0942-0.02770.1291-0.3023-0.1606-0.05830.1287-0.00650.02180.0925-0.03270.103381.82728.7636.302
132.1061.81531.66733.56162.3323.2305-0.0094-0.05480.0054-0.2315-0.03710.0003-0.0549-0.08820.04650.1661-0.02080.01170.08630.02730.013281.36418.3498.225
143.81981.5166-0.28422.3415-0.28692.2826-0.0289-0.11470.2074-0.20020.00380.021-0.18020.04380.02510.1822-0.0123-0.00160.0289-0.00330.014781.56520.4056.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 64
2X-RAY DIFFRACTION2A65 - 122
3X-RAY DIFFRACTION3A123 - 186
4X-RAY DIFFRACTION4A187 - 217
5X-RAY DIFFRACTION5A218 - 278
6X-RAY DIFFRACTION6A279 - 299
7X-RAY DIFFRACTION7A300 - 378
8X-RAY DIFFRACTION8B14 - 90
9X-RAY DIFFRACTION9B91 - 102
10X-RAY DIFFRACTION10B103 - 188
11X-RAY DIFFRACTION11B189 - 249
12X-RAY DIFFRACTION12B250 - 298
13X-RAY DIFFRACTION13B299 - 325
14X-RAY DIFFRACTION14B326 - 378

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