[English] 日本語
Yorodumi
- PDB-3toz: 2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3toz
Title2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NAD(P)-binding Rossmann-fold domain / Shikimate 5-dehydrogenase / NAD
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding
Similarity search - Function
Shikimate dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Shikimate dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMinasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.
Authors: Minasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
E: Shikimate dehydrogenase
F: Shikimate dehydrogenase
G: Shikimate dehydrogenase
H: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,77728
Polymers279,5608
Non-polymers6,21820
Water18,1951010
1
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6979
Polymers69,8902
Non-polymers1,8077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-108 kcal/mol
Surface area24830 Å2
MethodPISA
2
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2886
Polymers69,8902
Non-polymers1,3984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-47 kcal/mol
Surface area24390 Å2
MethodPISA
3
E: Shikimate dehydrogenase
F: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3486
Polymers69,8902
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-54 kcal/mol
Surface area24580 Å2
MethodPISA
4
G: Shikimate dehydrogenase
H: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4447
Polymers69,8902
Non-polymers1,5545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-65 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.130, 78.434, 214.829
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A and B, C and D, E and F, G and H represent Biological Assembly, dimer.

-
Components

#1: Protein
Shikimate dehydrogenase


Mass: 34944.953 Da / Num. of mol.: 8 / Fragment: Shikimate 5-dehydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: aroE, lmo0490 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8Y9N5, shikimate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3); Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG R3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 117864 / Num. obs: 117864 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5755 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NPD

1npd


Resolution: 2.2→29.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.282 / SU ML: 0.198
Isotropic thermal model: Atomic Thermal Factors Individually Refined.
Cross valid method: THROUGHOUT / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25584 5836 5 %RANDOM
Rwork0.19547 ---
all0.19855 110577 --
obs0.19855 110577 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.413 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å2-2.45 Å2
2--4.26 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17938 0 396 1010 19344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212573
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9925700
X-RAY DIFFRACTIONr_angle_other_deg0.856330944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.27452361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15925.209791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.635153392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6261575
X-RAY DIFFRACTIONr_chiral_restr0.0890.22926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023554
X-RAY DIFFRACTIONr_mcbond_it0.971.511617
X-RAY DIFFRACTIONr_mcbond_other0.2971.54796
X-RAY DIFFRACTIONr_mcangle_it1.634218757
X-RAY DIFFRACTIONr_scbond_it2.95137320
X-RAY DIFFRACTIONr_scangle_it4.2814.56943
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 383 -
Rwork0.261 8015 -
obs-8015 97.28 %
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)
11.11380.05840.15250.56390.02182.31490.02160.37540.20140.09860.0009-0.1163-0.0047-0.0341-0.02250.13970.0308-0.02490.13880.05070.22085.8276-0.978273.0379
23.75850.2981-2.3173.0446-0.53432.459-0.02920.7342-0.1991-0.15820.013-0.03250.34750.0730.01610.19450.0835-0.02960.5116-0.03960.14114.493-6.889648.9604
33.3201-0.09-0.66470.64290.32821.80770.23730.42380.4977-0.04950.0523-0.1696-0.2350.0679-0.28960.14790.01820.01710.09770.10390.302113.32189.709360.1187
41.4145-0.229-0.11920.66070.2331.8207-0.0436-0.36150.1885-0.02230.06880.0263-0.025-0.109-0.02520.03570.0226-0.0280.1076-0.04930.0929.7999-1.396105.5911
54.7052-0.4532-0.55182.21090.82762.99790.0339-0.9967-0.26760.0906-0.09890.01460.51510.17650.06510.13870.1214-0.01330.51610.01560.02262.7982-5.8747128.7337
63.02840.1655-1.52850.49340.38362.90270.0833-0.51860.4571-0.0451-0.03090.0264-0.2619-0.0884-0.05240.12650.0767-0.0490.1902-0.14350.20083.393410.0458117.3326
72.1147-0.0608-0.40350.7096-0.35414.47040.1177-0.46730.071-0.1524-0.0245-0.1755-0.0093-0.0425-0.09320.2134-0.0202-0.0090.11160.01560.328224.2125-34.369785.4067
83.635-0.01730.27161.7055-0.63951.17670.0669-1.01560.12470.0753-0.0346-0.0204-0.0464-0.2036-0.03240.0291-0.048-0.01030.3475-0.01040.014330.8651-37.7393110.6278
97.22271.70780.87960.6666-0.15858.52820.2176-0.1359-0.7579-0.05020.0214-0.24881.0302-0.6235-0.2390.3094-0.0648-0.03250.05110.01030.249920.9189-45.658189.0894
102.06860.4231-0.70330.52090.24732.94560.10470.64780.10340.03710.03890.0443-0.0520.0416-0.14360.14580.04230.00810.2810.0460.232530.805-33.820957.5219
115.17160.00321.36581.51380.22332.1453-0.14822.00730.6253-0.29170.07710.0261-0.32580.61880.07110.1787-0.0555-0.02721.06180.24840.127623.318-31.367232.1457
124.35110.30962.75531.13840.18372.73510.23490.9396-0.55980.02590.0627-0.06750.39290.4578-0.29760.13380.089-0.0140.3797-0.12850.106826.8151-45.542146.2464
130.73370.2020.38230.5385-0.01832.31310.0409-0.16460.0347-0.00970.03790.0283-0.1073-0.2785-0.07880.07740.03340.02570.08380.01130.1403-26.81836.999655.2836
141.38710.2083-0.10951.5849-0.02380.11630.0778-0.5088-0.06930.1116-0.0294-0.09380.09680.0659-0.04850.1246-0.0032-0.03030.21370.0330.1349-18.655-5.422472.5729
156.3897-3.76654.16832.3388-2.14535.5720.37470.1849-0.5006-0.0271-0.21680.27610.6748-0.3744-0.15790.3631-0.1108-0.01560.22470.05430.1803-31.5692-5.700550.1431
160.81680.08920.49170.24770.06392.4990.0150.2091-0.1143-0.01590.07890.03330.0758-0.0466-0.09390.10370.02970.01670.09370.0010.1386-23.59019.282417.319
172.32760.23030.60081.5792-0.16911.6733-0.01230.1173-0.0921-0.17260.09670.07040.05320.0744-0.08440.05350.00780.00560.0886-0.03710.0478-32.65016.1376-2.4701
184.22440.1129-1.58845.5559-1.60731.3821-0.0293-0.1248-0.4854-0.3731-0.096-0.54660.2286-0.18810.12530.39580.0611-0.07670.4262-0.00210.3788-19.1515-3.45317.6716
191.95750.2632-0.05560.61920.05742.12530.0069-0.4697-0.03350.02640.07640.10360.03020.1494-0.08340.07610.0413-0.02420.16910.0150.0856-5.0605-36.504536.1063
203.14210.6232-1.32724.3252-0.27084.261-0.1368-1.3024-0.42440.1390.08380.0610.5880.47960.05290.20080.1098-0.04970.72440.18470.0972-7.4338-42.80261.473
213.2487-0.2476-2.13240.48120.10642.81180.1839-0.61450.35490.00910.0680.0875-0.29080.3713-0.25190.1039-0.0110.00440.2507-0.08380.1285-11.0442-26.259249.1435
220.6926-0.11060.20051.0716-0.07452.4981-0.02970.04010.0294-0.05560.145-0.09190.0495-0.0321-0.11530.0452-0.007-0.0330.0271-0.00190.0993-10.5802-36.10259.5282
232.32240.5951-0.00140.7773-0.20652.54510.050.3083-0.1169-0.08390.039-0.0180.1264-0.1045-0.0890.0816-0.0012-0.0210.0515-0.00220.0771-5.7029-32.7748-18.667
243.6884-0.49730.96282.9385-1.1024.6034-0.0875-0.03180.35810.01790.0465-0.0001-0.4931-0.02250.0410.0912-0.0031-0.04810.05060.03040.1167-14.9802-24.31782.9179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2A160 - 209
3X-RAY DIFFRACTION3A210 - 291
4X-RAY DIFFRACTION4B2 - 165
5X-RAY DIFFRACTION5B166 - 213
6X-RAY DIFFRACTION6B214 - 291
7X-RAY DIFFRACTION7C5 - 132
8X-RAY DIFFRACTION8C133 - 262
9X-RAY DIFFRACTION9C263 - 291
10X-RAY DIFFRACTION10D3 - 153
11X-RAY DIFFRACTION11D154 - 232
12X-RAY DIFFRACTION12D233 - 291
13X-RAY DIFFRACTION13E3 - 192
14X-RAY DIFFRACTION14E193 - 267
15X-RAY DIFFRACTION15E268 - 291
16X-RAY DIFFRACTION16F5 - 166
17X-RAY DIFFRACTION17F167 - 268
18X-RAY DIFFRACTION18F269 - 291
19X-RAY DIFFRACTION19G1 - 168
20X-RAY DIFFRACTION20G169 - 205
21X-RAY DIFFRACTION21G206 - 291
22X-RAY DIFFRACTION22H1 - 119
23X-RAY DIFFRACTION23H120 - 265
24X-RAY DIFFRACTION24H266 - 291

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more