[English] 日本語
Yorodumi
- PDB-4ecd: 2.5 Angstrom Resolution Crystal Structure of Bifidobacterium long... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ecd
Title2.5 Angstrom Resolution Crystal Structure of Bifidobacterium longum Chorismate Synthase
ComponentsChorismate synthase
KeywordsLYASE / 4-Layer Sandwich / Chorismate synthase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding / cytosol
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLight, S.H. / Minasov, G. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.5 Angstrom Resolution Crystal Structure of Bifidobacterium longum Chorismate Synthase
Authors: Light, S.H. / Minasov, G. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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: Chorismate synthase
B: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4326
Polymers85,2912
Non-polymers1424
Water2,396133
1
A: Chorismate synthase
B: Chorismate synthase
hetero molecules

A: Chorismate synthase
B: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,86512
Polymers170,5814
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area9800 Å2
ΔGint-112 kcal/mol
Surface area43290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.944, 123.944, 97.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Chorismate synthase / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 42645.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: aroC, BLIJ_1653, Blon_1598 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7GS97, chorismate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (PH 8.3). Screen: 0.2 M Sodium bromide, 0.1 M Bis-tris propane, 20% (w/v) Peg 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 26509 / Num. obs: 26509 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1352 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G85

2g85


Resolution: 2.5→29.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.524 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25347 1312 5 %RANDOM
Rwork0.19702 ---
obs0.19979 25009 97.6 %-
all-25009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 4 133 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194052
X-RAY DIFFRACTIONr_bond_other_d0.0010.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9815477
X-RAY DIFFRACTIONr_angle_other_deg0.93836660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0415537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87423.006163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76115680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8641543
X-RAY DIFFRACTIONr_chiral_restr0.0960.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 87 -
Rwork0.278 1670 -
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)
127.8905-2.462-8.62930.35441.04433.28340.4706-0.5834-0.3872-0.0121-0.149-0.1438-0.0606-0.1548-0.32160.2847-0.0089-0.02690.35380.14960.379220.5886-23.341243.9542
20.67250.03480.23231.12060.77880.79770.0851-0.03790.0432-0.1757-0.10130.0173-0.209-0.14230.01620.3570.03880.01480.22710.03550.197317.3991-15.352434.9294
315.85180.69143.83350.1850.20950.93860.99712.3809-4.5296-0.4939-0.0113-0.20440.0690.5134-0.98581.89310.8885-0.22630.7351-0.67681.295516.9067-33.153710.4856
45.1470.52442.50930.82730.02662.1540.40080.70640.3153-0.4824-0.29870.205-0.13790.0589-0.10210.770.4449-0.00060.50970.0680.106812.7433-23.87813.6636
50.5406-0.0754-0.81280.49990.03191.29240.22160.10440.0082-0.2905-0.1201-0.0828-0.2341-0.1011-0.10160.35350.0837-0.03930.1874-0.00350.246224.3845-30.215325.2667
62.1626-0.461-1.05290.8965-0.32110.8872-0.008-0.05460.0084-0.0760.03250.01840.0537-0.0089-0.02450.33610.03670.01880.2661-0.0020.229925.2275-35.212729.9803
76.7244-9.77729.116314.2725-13.261612.36140.86550.81390.7691-1.6146-1.6169-0.87581.54511.09110.75140.5333-0.40620.1581.3172-0.57251.136830.5643-37.522814.8677
80.44010.4659-0.23481.5120.24370.60030.1506-0.06170.043-0.2699-0.1049-0.1098-0.127-0.0239-0.04570.35050.00120.0720.22560.01770.24729.3492-23.299729.0402
91.75061.1966-0.80371.20510.20262.05630.0955-0.1614-0.0506-0.03320.0031-0.0931-0.11630.1005-0.09860.3027-0.00410.02930.27720.03650.228539.8021-48.205646.4713
101.79020.67162.45030.87541.85416.22340.10720.1083-0.54630.02150.1381-0.23920.35470.5934-0.24530.33540.02870.01490.20410.04260.394142.4245-59.003340.652
110.893-0.24540.5460.50490.1870.60920.034-0.0674-0.1107-0.03540.00180.02250.0181-0.0038-0.03580.3063-0.0130.03130.24110.03560.260134.0523-53.956141.6553
121.2058-0.5606-1.97870.5461.19325.15480.18810.1029-0.3831-0.126-0.11960.1119-0.1064-0.1077-0.06850.34440.0352-0.08440.1593-0.07650.394126.9424-60.340920.7102
130.63830.88120.12431.28530.14210.0665-0.0142-0.0511-0.1161-0.09980.0111-0.0939-0.0195-0.1050.00310.34380.0474-0.0130.22470.00120.269623.9806-48.525132.1631
141.697-0.2502-0.12471.1029-0.02360.0134-0.041-0.097-0.0202-0.17490.04370.0783-0.0114-0.0105-0.00270.30010.0278-0.01440.2432-0.01620.27120.8955-43.022132.2201
151.9924-0.2104-0.91940.02450.15883.5869-0.0063-0.1569-0.2485-0.01090.01520.0363-0.10270.1323-0.00890.31340.01930.03440.2147-0.00420.276129.3515-48.574137.0064
1614.6532-1.04693.38133.80210.35930.9032-0.1472-0.9659-0.50430.11870.31280.1131-0.0153-0.2721-0.16550.1874-0.05330.08040.45520.17850.194718.2297-53.545456.1295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 10
2X-RAY DIFFRACTION2A11 - 170
3X-RAY DIFFRACTION3A171 - 177
4X-RAY DIFFRACTION4A178 - 210
5X-RAY DIFFRACTION5A211 - 240
6X-RAY DIFFRACTION6A241 - 267
7X-RAY DIFFRACTION7A268 - 296
8X-RAY DIFFRACTION8A297 - 389
9X-RAY DIFFRACTION9B1 - 28
10X-RAY DIFFRACTION10B29 - 64
11X-RAY DIFFRACTION11B65 - 171
12X-RAY DIFFRACTION12B172 - 211
13X-RAY DIFFRACTION13B212 - 238
14X-RAY DIFFRACTION14B239 - 315
15X-RAY DIFFRACTION15B316 - 372
16X-RAY DIFFRACTION16B373 - 389

+
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