[English] 日本語
Yorodumi
- PDB-4rcv: M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rcv
TitleM. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase bound to 1-deoxy-L-erythrulose
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / Reductoisomerase
Function / homology
Function and homology information


terpenoid biosynthetic process, mevalonate-independent / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / cobalt ion binding / NADPH binding / manganese ion binding / magnesium ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-deoxy-L-erythrulose / : / Chem-NDP / PHOSPHITE ION / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsGulick, A.M. / Allen, C.L. / Kholodar, S.A. / Murkin, A.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces.
Authors: Kholodar, S.A. / Allen, C.L. / Gulick, A.M. / Murkin, A.S.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7979
Polymers84,9342
Non-polymers1,8637
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-28 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.370, 64.378, 85.741
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4- ...DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4-phosphate synthase


Mass: 42466.914 Da / Num. of mol.: 2 / Fragment: UNP residues 1-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: dxr, P425_02990, RVBD_2870c / Production host: Escherichia coli (E. coli)
References: UniProt: I6YAH0, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

-
Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-DE2 / 1-deoxy-L-erythrulose


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3
#5: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3
#6: 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG3500, 25 mM sodium acetate, 25 mM Bis-Tris, 1% Tacsimate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.294→83.95 Å / Num. all: 32389 / Num. obs: 32321 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.6
Reflection shellResolution: 2.294→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A03

4a03


Resolution: 2.294→35.161 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1636 5.07 %RANDOM
Rwork0.1728 ---
obs0.1758 32295 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.294→35.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 87 133 5647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015641
X-RAY DIFFRACTIONf_angle_d1.1517729
X-RAY DIFFRACTIONf_dihedral_angle_d15.2071971
X-RAY DIFFRACTIONf_chiral_restr0.071916
X-RAY DIFFRACTIONf_plane_restr0.0061009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.294-2.36110.28871150.2052461X-RAY DIFFRACTION97
2.3611-2.43730.27321590.18462562X-RAY DIFFRACTION100
2.4373-2.52440.26241140.19172560X-RAY DIFFRACTION100
2.5244-2.62540.26031380.18452524X-RAY DIFFRACTION100
2.6254-2.74490.28371420.19132554X-RAY DIFFRACTION100
2.7449-2.88950.29711500.18232547X-RAY DIFFRACTION100
2.8895-3.07050.25541230.18312581X-RAY DIFFRACTION100
3.0705-3.30740.25331320.1722549X-RAY DIFFRACTION100
3.3074-3.63990.21811270.16192561X-RAY DIFFRACTION100
3.6399-4.16590.18771420.14972568X-RAY DIFFRACTION100
4.1659-5.24580.20031460.1582563X-RAY DIFFRACTION100
5.2458-35.16550.21321480.1812629X-RAY DIFFRACTION99

+
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://pdbjlc1.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