[English] 日本語
Yorodumi
- PDB-4mpq: Crystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mpq
TitleCrystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis ATCC 23457
ComponentsDihydrodipicolinate synthetase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dihydrodipicolinate synthetase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis ATCC 23457
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lukacz, C. / Lorimer, D. / Edwards, T.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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: Dihydrodipicolinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7222
Polymers35,6601
Non-polymers621
Water7,044391
1
A: Dihydrodipicolinate synthetase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)214,33112
Polymers213,9596
Non-polymers3726
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area15660 Å2
ΔGint-17 kcal/mol
Surface area63940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.060, 95.060, 125.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-837-

HOH

31A-855-

HOH

-
Components

#1: Protein Dihydrodipicolinate synthetase


Mass: 35659.777 Da / Num. of mol.: 1 / Fragment: BrmeB.01563.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biotype 2 (strain ATCC 23457) / Gene: BM28_B0232, BMEA_B0240 / Plasmid: BrmeB.01563.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RKH4, EC: 3.5.4.22
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EmeraldBio MCSG1 screen, a11: 10% PEG 4000, 200mM MgCl2, 100mM MES/NaOH pH 6.5; cryo 20% EG; BrmeB.01563.a.B1.PS01874 at 19.3mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 8, 2013 / Details: RIGAKU VARIMAX
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 34409 / Num. obs: 34293 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 25.711 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.80.4853.13100432453198.3
1.8-1.840.4083.73101652387199
1.84-1.90.3754.08105672383199.5
1.9-1.960.2566.17104892260199.7
1.96-2.020.227.33107992240199.8
2.02-2.090.1799.161085621631100
2.09-2.170.13912.991229020851100
2.17-2.260.12416.25135272007199.9
2.26-2.360.1118.25135851935199.8
2.36-2.470.09521.11137131851199.9
2.47-2.610.08623.93140961778199.9
2.61-2.770.079271466116861100
2.77-2.960.06733.921642016011100
2.96-3.20.05339.951564414821100
3.2-3.50.04146.81145981383199.9
3.5-3.910.03558.1130521253199.9
3.91-4.520.02969.541155411241100
4.52-5.530.0363.0298189681100
5.53-7.830.03653.4976857841100
7.83-500.02374.483934470196.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.96 Å
Translation3.5 Å19.96 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2hmc

2hmc


Resolution: 1.75→44.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1548 / WRfactor Rwork: 0.1324 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8874 / SU B: 3.795 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1046 / SU Rfree: 0.0979 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 1732 5.1 %RANDOM
Rwork0.1586 ---
all0.1599 34409 --
obs0.1599 34269 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.86 Å2 / Biso mean: 20.2893 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.15 Å20 Å2
2--0.15 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 4 391 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192551
X-RAY DIFFRACTIONr_bond_other_d0.0010.022430
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9563474
X-RAY DIFFRACTIONr_angle_other_deg0.81935580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70923.67109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5215403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.741516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_mcbond_it0.9861.4111320
X-RAY DIFFRACTIONr_mcbond_other0.9721.411319
X-RAY DIFFRACTIONr_mcangle_it1.5862.1131654
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 113 -
Rwork0.22 2331 -
all-2444 -
obs-2453 98.23 %
Refinement TLS params.Method: refined / Origin x: 4.506 Å / Origin y: 31.186 Å / Origin z: 12.637 Å
111213212223313233
T0.0211 Å2-0.0021 Å20.0151 Å2-0.0126 Å2-0.0088 Å2--0.0176 Å2
L0.2079 °2-0.0652 °20.0015 °2-0.5328 °2-0.3609 °2--0.4557 °2
S-0.0239 Å °0.0006 Å °-0.0163 Å °0.0012 Å °-0.0201 Å °-0.0214 Å °0.041 Å °0.0067 Å °0.044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 320
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 891

+
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