[English] 日本語
Yorodumi
- PDB-3qfe: Crystal structures of a putative dihydrodipicolinate synthase fam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qfe
TitleCrystal structures of a putative dihydrodipicolinate synthase family protein from Coccidioides immitis
ComponentsPutative dihydrodipicolinate synthase family protein
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Coccidioides / Valley Fever / Coccidioidomycosis / pathogenic fungus / soil-born pathogen / putative uncharacterized protein
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structures of a putative dihydrodipicolinate synthase family protein from Coccidioides immitis
Authors: Edwards, T.E. / Gardberg, A.S. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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 / _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: Putative dihydrodipicolinate synthase family protein
B: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,57012
Polymers67,1532
Non-polymers41710
Water3,369187
1
A: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7235
Polymers33,5771
Non-polymers1464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8477
Polymers33,5771
Non-polymers2716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.760, 89.760, 371.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-317-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 1 - 313 / Label seq-ID: 5 - 317

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

-
Components

#1: Protein Putative dihydrodipicolinate synthase family protein


Mass: 33576.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_00151 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CoimA.00447.a.A1 PW28367 at 24.64 mg/mL against CSHT screen condition B2, 0.2 M CaCl2, 0.1 M Na Hepes pH 7.5, 28% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 38337 / Num. obs: 38200 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 19.7 % / Biso Wilson estimate: 46.203 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.2
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.35-2.4117.80.5135.674882627492749100
2.41-2.480.4856.33487442689100
2.48-2.550.4716.89475062639100
2.55-2.630.368.54473812538100
2.63-2.710.3429.83453972462100
2.71-2.810.25212.24465582406100
2.81-2.910.18916.1455902309100
2.91-3.030.16118.83446752236100
3.03-3.170.13722.21438792159100
3.17-3.320.10927.95419212072100
3.32-3.50.09135.4389171964100
3.5-3.720.07540.9336666188399.4
3.72-3.970.06446.2934415174799.4
3.97-4.290.05653.61354561677100
4.29-4.70.04860.57331091542100
4.7-5.250.04958.94307491408100
5.25-6.070.05256.37277861267100
6.07-7.430.04761.57254101102100
7.43-10.510.03572.2919253882100
10.510.03466.48902746980.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.05 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.87 Å
Translation3 Å19.87 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v8z

2v8z


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2213 / WRfactor Rwork: 0.1901 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8642 / SU B: 12.502 / SU ML: 0.136 / SU R Cruickshank DPI: 0.2443 / SU Rfree: 0.2002 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1902 5 %RANDOM
Rwork0.1993 ---
obs0.201 38011 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.46 Å2 / Biso mean: 40.6171 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å21.17 Å20 Å2
2--2.34 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 16 187 4596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224512
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9786168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19523.397156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6851525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223420
X-RAY DIFFRACTIONr_mcbond_it0.7481.53041
X-RAY DIFFRACTIONr_mcangle_it1.424852
X-RAY DIFFRACTIONr_scbond_it2.04131471
X-RAY DIFFRACTIONr_scangle_it3.3724.51313
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2130 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.365
LOOSE THERMAL2.8610
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 144 -
Rwork0.227 2585 -
all-2729 -
obs--99.38 %
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)
10.9869-0.3350.73820.8645-0.28822.75340.00230.02310.1443-0.0404-0.0739-0.0824-0.33570.28330.07160.0886-0.0840.00510.10280.00850.043214.3277-38.1394-12.9132
21.1175-0.6958-0.13471.64560.1481.85610.01830.0237-0.0085-0.0271-0.12220.1165-0.09-0.05110.10390.0197-0.006-0.00070.0268-0.02890.035442.4806-15.672-15.0522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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