[English] 日本語
Yorodumi
- PDB-3rmj: Crystal structure of truncated alpha-Isopropylmalate Synthase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rmj
TitleCrystal structure of truncated alpha-Isopropylmalate Synthase from Neisseria meningitidis
Components2-isopropylmalate synthase
KeywordsTRANSFERASE / 2-Isopropylmalate Synthase / LeuA / Truncation / Neisseria meningitidis / TIM Barrel / Catalytic Domain / Dimer / Leucine Biosynthesis / Alpha-Ketoisovalerate / Acetyl Coenzyme A
Function / homology
Function and homology information


2-isopropylmalate synthase / 2-isopropylmalate synthase activity / L-leucine biosynthetic process / cytosol
Similarity search - Function
2-isopropylmalate synthase, bacterial-type / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like ...2-isopropylmalate synthase, bacterial-type / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / 2-isopropylmalate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHuisman, F.H.A. / Baker, H.M. / Koon, N. / Baker, E.N. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2012
Title: Removal of the C-terminal regulatory domain of alpha-isopropylmalate synthase disrupts functional substrate binding
Authors: Huisman, F.H.A. / Koon, N. / Bulloch, E.M.M. / Baker, H.M. / Baker, E.N. / Squire, C.J. / Parker, E.J.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 1, 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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-isopropylmalate synthase
B: 2-isopropylmalate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58211
Polymers79,9632
Non-polymers6199
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-24 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.296, 103.581, 129.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 2-isopropylmalate synthase / Alpha-IPM synthase / Alpha-isopropylmalate synthase


Mass: 39981.496 Da / Num. of mol.: 2 / Fragment: N-terminal region, UNP residues 1-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: Serogroup B / Gene: leuA, NMB1070 / Plasmid: pE365Term / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9JZG1, 2-isopropylmalate synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Mg acetate, 20% MPEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 18K, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9546 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9546 Å / Relative weight: 1
ReflectionResolution: 1.8→21.81 Å / Num. all: 56627 / Num. obs: 56515 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.01191 / Mean I/σ(I) obs: 1.1 / Num. unique all: 8096 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.6.0111refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SR9

1sr9


Resolution: 1.95→21.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.173 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19052 2347 5.1 %RANDOM
Rwork0.15824 ---
all0.15994 46485 --
obs0.15994 44041 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 34 332 5006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9646559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10824.615195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62215839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213591
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 145 -
Rwork0.205 2976 -
obs--99.97 %
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)
10.646-0.0349-0.06810.0394-0.10451.4292-0.01040.01090.0415-0.0135-0.0078-0.0215-0.0687-0.2240.01820.1070.005-0.020.07440.02550.026337.40570.2018.694
21.4176-0.61590.84220.9409-0.76771.86310.03540.0433-0.0776-0.07150.0050.01710.16030.0139-0.04040.1194-0.0128-0.00650.01930.0140.021851.01360.4324.923
30.0606-0.0701-0.23870.48250.01911.2494-0.006-0.02970.00980.0561-0.0079-0.0646-0.01810.09710.01390.1037-0.01-0.03080.06670.01340.023951.79465.71921.918
41.1469-0.13860.61641.5647-0.14272.6218-0.0305-0.06930.15680.19160.12890.0785-0.4332-0.4882-0.09830.20230.11840.01270.14960.02860.048233.97576.90529.342
50.65060.0925-0.40540.2583-0.19011.0238-0.02140.03740.01250.00620.00520.04980.0542-0.07590.01620.1106-0.00180.00120.0431-0.0240.025130.39757.34253.239
61.66151.3421-0.16341.8805-0.21330.5295-0.017-0.09910.17830.0165-0.04190.15270.003-0.00930.0590.12790.0141-0.01190.0434-0.02580.036240.51969.56463.616
70.0577-0.0912-0.00460.53570.26531.0657-0.01510.00270.0246-0.0338-0.0029-0.0342-0.02490.08260.0180.10120.0057-0.00760.0624-0.00580.012248.2465.06946.7
81.40330.2672-0.92130.5811-0.34211.7685-0.08730.2476-0.0453-0.0909-0.0039-0.01620.317-0.25540.09120.159-0.0305-0.00230.092-0.02480.012634.29351.83734.074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 83
2X-RAY DIFFRACTION2A84 - 147
3X-RAY DIFFRACTION3A148 - 259
4X-RAY DIFFRACTION4A260 - 324
5X-RAY DIFFRACTION5B4 - 75
6X-RAY DIFFRACTION6B76 - 143
7X-RAY DIFFRACTION7B144 - 259
8X-RAY DIFFRACTION8B260 - 324

+
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://pdbjlvh1.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