[English] 日本語
Yorodumi
- PDB-5ex4: 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ex4
Title3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites
Components3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
KeywordsTRANSFERASE / shikimate pathway / allosteric regulation
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHOSPHATE ION / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsReichau, S. / Jiao, W. / Blackmore, N.J. / Hutton, R.D. / Parker, E.J.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
New Zealand Marsden FundUOC1105 New Zealand
Maurice Wilkins Centre for Molecular Biodiscovery New Zealand
CitationJournal: to be published
Title: 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites
Authors: Reichau, S. / Blackmore, N.J. / Jiao, W. / Parker, E.J.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,66619
Polymers101,6572
Non-polymers2,00917
Water12,737707
1
A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules

A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,33238
Polymers203,3144
Non-polymers4,01834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area18610 Å2
ΔGint-247 kcal/mol
Surface area62260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.680, 204.680, 66.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase


Mass: 50828.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E8NFD1, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase

-
Non-polymers , 7 types, 724 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M TRIS-HCL, PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL, 1 MILLIM L-TRYPTOPHAN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9357 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 2.25→44.24 Å / Num. all: 76066 / Num. obs: 76066 / % possible obs: 100 % / Redundancy: 10.8 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.131 / Rsym value: 0.125 / Net I/av σ(I): 4.789 / Net I/σ(I): 14.2 / Num. measured all: 818010
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.25-2.3710.50.3722115999110470.120.3726.2100
2.37-2.5210.70.292.6111050104140.0930.297.6100
2.52-2.6910.90.2263.310713998600.0720.2269.5100
2.69-2.9110.1674.410114991830.0530.16712.2100
2.9-3.18110.1275.69251384160.040.12715.1100
3.18-3.5610.90.1086.18290176100.0340.10818.4100
3.56-4.1110.70.1026.17290067940.0330.10222.3100
4.11-5.0310.10.0916.75767957340.030.09123.7100
5.03-7.1210.90.07384887244710.0230.07323.7100
7.12-44.314110.0619.12780825370.0190.06127.399.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
MOLREPphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B7O

2b7o


Resolution: 2.25→44.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1428 / FOM work R set: 0.9249 / SU B: 2.677 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0308 / SU Rfree: 0.0277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 3788 5 %RANDOM
Rwork0.1406 ---
obs0.1421 72258 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 26.286 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2.25→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7088 0 128 707 7923
Biso mean--32.88 37.12 -
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197577
X-RAY DIFFRACTIONr_bond_other_d0.0010.027180
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.95910319
X-RAY DIFFRACTIONr_angle_other_deg0.73316447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36423.324352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.415151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4131572
X-RAY DIFFRACTIONr_chiral_restr0.090.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021753
X-RAY DIFFRACTIONr_mcbond_it3.152.3553827
X-RAY DIFFRACTIONr_mcbond_other3.1472.3553826
X-RAY DIFFRACTIONr_mcangle_it4.6413.5134793
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 278 -
Rwork0.154 5302 -
all-5580 -
obs--99.93 %

+
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