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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ooe
TitleM. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W203Y mutant bound to fosmidomycin and NADPH
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / reductoisomerase / OXIDOREDUCTASE-ANTIBIOTIC complex
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
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / : / Chem-NDP / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.826 Å
AuthorsAllen, C.L. / Kholodar, S.A. / Murkin, A.S. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2014
Title: Alteration of the Flexible Loop in 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition by Fosmidomycin.
Authors: Kholodar, S.A. / Tombline, G. / Liu, J. / Tan, Z. / Allen, C.L. / Gulick, A.M. / Murkin, A.S.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: 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_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_label_asym_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_label_asym_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
C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
D: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,70916
Polymers169,7764
Non-polymers3,93412
Water30,1031671
1
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)86,8558
Polymers84,8882
Non-polymers1,9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-54 kcal/mol
Surface area26880 Å2
MethodPISA
2
C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
D: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8558
Polymers84,8882
Non-polymers1,9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-51 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.270, 114.240, 133.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#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: 42443.879 Da / Num. of mol.: 4 / Fragment: UNP residues 1-389 / Mutation: W203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dxr, RVBD_2870c / Production host: Escherichia coli (E. coli)
References: UniProt: I6YAH0, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical
ChemComp-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1671 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6% PEG4000, 50 mM MES, 20% MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.284 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 1.826→86.712 Å / Num. all: 151359 / Num. obs: 145456 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16
Reflection shellResolution: 1.826→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.8 / Num. unique all: 18847 / % possible all: 86.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A03

4a03


Resolution: 1.826→38.827 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1949 1.37 %RANDOM
Rwork0.1697 ---
all0.1703 151777 --
obs0.1703 142154 93.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.826→38.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 240 1671 12931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711550
X-RAY DIFFRACTIONf_angle_d1.15315834
X-RAY DIFFRACTIONf_dihedral_angle_d16.4884088
X-RAY DIFFRACTIONf_chiral_restr0.0711865
X-RAY DIFFRACTIONf_plane_restr0.0052066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.826-1.87220.3387990.25577360X-RAY DIFFRACTION69
1.8722-1.92280.27471290.22319251X-RAY DIFFRACTION88
1.9228-1.97930.25991450.203710040X-RAY DIFFRACTION95
1.9793-2.04320.23481290.191310241X-RAY DIFFRACTION96
2.0432-2.11630.2261510.180810229X-RAY DIFFRACTION96
2.1163-2.2010.21611410.174210342X-RAY DIFFRACTION98
2.201-2.30110.19521410.172510287X-RAY DIFFRACTION97
2.3011-2.42240.21131470.171110417X-RAY DIFFRACTION98
2.4224-2.57420.22221500.178410347X-RAY DIFFRACTION97
2.5742-2.77290.21891450.17710303X-RAY DIFFRACTION96
2.7729-3.05180.22461400.173310390X-RAY DIFFRACTION97
3.0518-3.49320.21151470.161710392X-RAY DIFFRACTION97
3.4932-4.40010.17771420.140710343X-RAY DIFFRACTION95
4.4001-38.83610.17611430.150210263X-RAY DIFFRACTION92

+
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