[English] 日本語
Yorodumi
- PDB-5j6f: Crystal structure of DAH7PS-CM complex from Geobacillus sp. with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j6f
TitleCrystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate
Components3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
KeywordsTRANSFERASE / ISOMERASE / tim barrel / dah7ps / dah7p / lyase
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process / metal ion binding
Similarity search - Function
Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PREPHENIC ACID / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
Similarity search - Component
Biological speciesGeobacillus sp. GHH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsNazmi, A.R. / Othman, M. / Lang, E.J.M. / Bai, Y. / Allison, T.M. / Panjkar, S. / Arcus, V.L. / Parker, E.J.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate.
Authors: Nazmi, A.R. / Lang, E.J.M. / Bai, Y. / Allison, T.M. / Othman, M.H. / Panjikar, S. / Arcus, V.L. / Parker, E.J.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,81710
Polymers82,8712
Non-polymers9468
Water00
1
A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules

A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,63520
Polymers165,7424
Non-polymers1,89316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area29280 Å2
ΔGint-296 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.438, 95.438, 167.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 3 - 354 / Label seq-ID: 3 - 354

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3


Mass: 41435.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. GHH01 (bacteria) / Gene: aroA, GHH_c28860 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: L8A208, 3-deoxy-7-phosphoheptulonate synthase, chorismate mutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PRE / PREPHENIC ACID


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.7 % / Mosaicity: 0.36 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 ...Details: A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→82.65 Å / Num. obs: 22482 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.887.71.3361100
9.12-83.737.10.019198.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.1.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFC

3tfc


Resolution: 2.75→82.65 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 38.682 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1054 4.7 %RANDOM
Rwork0.18221 ---
obs0.18471 21178 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å2-0 Å2
2---0.49 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.75→82.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 54 0 5420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195490
X-RAY DIFFRACTIONr_bond_other_d0.0070.025404
X-RAY DIFFRACTIONr_angle_refined_deg2.121.987418
X-RAY DIFFRACTIONr_angle_other_deg1.5112.99912392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67724.549255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84115987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681543
X-RAY DIFFRACTIONr_chiral_restr0.1070.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026217
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021194
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7294.6812765
X-RAY DIFFRACTIONr_mcbond_other2.7264.682764
X-RAY DIFFRACTIONr_mcangle_it4.2897.0213451
X-RAY DIFFRACTIONr_mcangle_other4.2897.0223452
X-RAY DIFFRACTIONr_scbond_it3.8955.292725
X-RAY DIFFRACTIONr_scbond_other3.8945.2922726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.267.7463968
X-RAY DIFFRACTIONr_long_range_B_refined7.98137.4586141
X-RAY DIFFRACTIONr_long_range_B_other7.98337.4476140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 39524 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 75 -
Rwork0.34 1561 -
obs--99.21 %
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)
10.86210.2912-0.51231.7703-1.92725.21790.00460.1040.0358-0.0384-0.13210.2702-0.1823-0.24490.12750.28080.0160.00830.2359-0.12860.2768-50.26128.5123.755
223.4021.7302-2.41253.2927-2.62793.3441-0.7540.3235-1.0869-0.32060.66940.020.9052-0.53910.08460.95880.0379-0.0120.4238-0.20550.6121-30.05216.4731.093
31.8440.4838-0.27220.96720.05251.28310.00160.1211-0.3245-0.2258-0.1014-0.18850.18670.18790.09990.47920.19390.0820.110.0050.1562-12.03329.1590.559
41.2312-0.54120.53343.01351.19631.60370.06690.00480.0912-0.233-0.1058-0.1244-0.25660.2860.03880.2607-0.0918-0.05860.30050.12420.31132.60859.72331.352
5129.05518.7477-22.883311.44660.76524.5756.358-10.662517.35590.3607-3.54253.2382-1.02521.2656-2.81551.6596-0.85550.89592.0642-1.57653.55333.30937.60839.996
61.85361.2275-0.35292.8322-0.21142.11450.2298-0.2843-0.1680.292-0.3882-0.19760.10420.18130.15840.34160.0331-0.03390.15310.09720.183-18.7924.51135.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 91
2X-RAY DIFFRACTION2A92 - 108
3X-RAY DIFFRACTION3A109 - 354
4X-RAY DIFFRACTION4B1 - 87
5X-RAY DIFFRACTION5B102 - 103
6X-RAY DIFFRACTION6B104 - 354

+
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