[English] 日本語
Yorodumi
- PDB-4jti: Crystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jti
TitleCrystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM BARREL / LIPOPOLYSACCHARIDE BIOSYNTHESIS
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAllison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2013
Title: Examining the Role of Intersubunit Contacts in Catalysis by 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase.
Authors: Allison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J.
History
DepositionMar 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Sep 20, 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: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
C: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8189
Polymers121,6414
Non-polymers1775
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-106 kcal/mol
Surface area35470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.670, 85.200, 162.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
2-dehydro-3-deoxyphosphooctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDO 8-P synthase ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDO 8-P synthase / KDOPS / Phospho-2-dehydro-3-deoxyoctonate aldolase


Mass: 30410.158 Da / Num. of mol.: 4 / Mutation: F114R, R117Q, F139G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: kdsA, NMB1283 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 1.6 M NaCl, cryoprotectant 20% glycerol and the reservoir solution, VAPOR ...Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 1.6 M NaCl, cryoprotectant 20% glycerol and the reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.75→40.835 Å / Num. all: 115042 / Num. obs: 115042 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.088 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.847.30.4191.8121025166410.419100
1.84-1.967.30.2582.9114289157110.258100
1.96-2.097.30.1744.1107713148440.174100
2.09-2.267.20.1235.3100083138170.123100
2.26-2.477.20.094791795127410.094100
2.47-2.777.10.0827.482603115730.082100
2.77-3.27.10.0876.572489102760.087100
3.2-3.916.70.0856.65826387240.085100
3.91-5.5370.0638.64758168320.063100
5.53-40.8356.90.0618.32689438830.06198.5

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QKF

2qkf


Resolution: 1.75→40.82 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2025 / WRfactor Rwork: 0.1711 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.897 / SU B: 3.665 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0964 / SU Rfree: 0.0944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 5751 5 %RANDOM
Rwork0.159 ---
obs0.1604 114951 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.58 Å2 / Biso mean: 28.5823 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å2-0 Å2
2--0.6 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 5 716 8584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0198027
X-RAY DIFFRACTIONr_bond_other_d0.0120.028008
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.97710869
X-RAY DIFFRACTIONr_angle_other_deg1.855318438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82751034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59525.241332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.525151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.951532
X-RAY DIFFRACTIONr_chiral_restr0.1130.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219036
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021728
X-RAY DIFFRACTIONr_mcbond_it2.2931.944106
X-RAY DIFFRACTIONr_mcbond_other2.2931.9384105
X-RAY DIFFRACTIONr_mcangle_it3.3162.8825120
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 419 -
Rwork0.196 7980 -
all-8399 -
obs--100 %
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)
10.95550.0636-0.36180.4172-0.02270.7892-0.06250.20450.0246-0.03140.0256-0.0076-0.0045-0.17230.03690.008-0.0056-0.00180.0910.00250.00577.96620.58847.756
20.3479-0.23120.18020.4542-0.01250.6905-0.016-0.05070.04490.01830.0110.00010.035-0.06590.00490.0186-0.0110.01130.0537-0.01280.025115.57213.91983.604
30.308-0.109-0.03350.2476-0.12010.8322-0.0326-0.03210.0215-0.06520.0094-0.0198-0.0079-0.03910.02320.0518-0.00330.00610.0276-0.01590.010333.58-1.46337.768
40.3388-0.471-0.30741.16650.49920.9834-0.0865-0.0111-0.03030.23160.05640.050.23750.08380.03010.10520.03950.00820.0212-0.00690.016937.8-11.53573.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 277
2X-RAY DIFFRACTION2B1 - 279
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D1 - 277

+
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