[English] 日本語
Yorodumi
- PDB-2qmw: The crystal structure of the prephenate dehydratase (PDT) from St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qmw
TitleThe crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus subsp. aureus Mu50
ComponentsPrephenate dehydratase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC85812 / prephenate dehydratase (PDT) / Staphylococcus aureus subsp. aureus Mu50 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process
Similarity search - Function
Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain / ACT domain profile. / ACT domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits ...Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Prephenate dehydratase / Prephenate dehydratase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsTan, K. / Zhang, R. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Structures of open (R) and close (T) states of prephenate dehydratase (PDT) - implication of allosteric regulation by L-phenylalanine.
Authors: Tan, K. / Li, H. / Zhang, R. / Gu, M. / Clancy, S.T. / Joachimiak, A.
History
DepositionJul 17, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionAug 7, 2007ID: 2IQ8
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,3187
Polymers60,0062
Non-polymers3125
Water1,74797
1
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules

A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,63714
Polymers120,0124
Non-polymers62510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.859, 87.406, 107.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe Chain A forms a dimer with its symmetry-related molecule (1-x,1-y,z). Similarly, the Chain B forms a dimer with its symmetry-related molecule (1-x,1-y,z). The two dimers form a tetramer.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Prephenate dehydratase / / PDT


Mass: 30002.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: Mu50 / Gene: SAV1915 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99SX2, UniProt: A0A0H3K044*PLUS

-
Non-polymers , 5 types, 102 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium citrate, 3M Sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97942
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2006 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979421
ReflectionResolution: 2.3→45.88 Å / Num. all: 25930 / Num. obs: 25930 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 56.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1672 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.88 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.418 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.383 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 1320 5.1 %RANDOM
Rwork0.22488 ---
all0.22734 24569 --
obs0.22734 24569 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.484 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 20 97 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1141.9475621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4025506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0225.233193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.46315674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8091510
X-RAY DIFFRACTIONr_chiral_restr0.1750.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023124
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21961
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.22805
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.150.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1241.52554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99524140
X-RAY DIFFRACTIONr_scbond_it3.06331622
X-RAY DIFFRACTIONr_scangle_it4.4744.51481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 88 -
Rwork0.219 1728 -
obs--94.73 %
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)
10.28410.24650.03470.61660.20080.3706-0.0076-0.00960.0584-0.0267-0.02560.09320.0082-0.01290.0333-0.0592-0.0007-0.012-0.0623-0.00440.055122.395349.189945.4716
20.3956-0.2055-0.80270.11510.35582.0814-0.046-0.07990.0130.1193-0.0223-0.05650.20330.0870.06830.0725-0.0292-0.01110.0115-0.0274-0.155232.763933.8258-15.5051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2644 - 267
2X-RAY DIFFRACTION2BB1 - 2644 - 267

+
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