[English] 日本語
Yorodumi
- PDB-4ol9: Crystal Structure of putative 2-dehydropantoate 2-reductase PanE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ol9
TitleCrystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate
ComponentsPutative 2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ketopantoate reductase
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytosol / cytoplasm
Similarity search - Function
: / Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...: / Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / 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
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXAMIC ACID / 2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate
Authors: Dranow, D.M. / Wernimont, A.K. / Abendroth, A. / Pierce, P.G. / Bullen, J. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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: Putative 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2326
Polymers32,2131
Non-polymers1,0195
Water5,098283
1
A: Putative 2-dehydropantoate 2-reductase
hetero molecules

A: Putative 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,46412
Polymers64,4262
Non-polymers2,03810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6870 Å2
ΔGint-24 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.590, 108.520, 47.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Putative 2-dehydropantoate 2-reductase / Ketopantoate reductase / KPA reductase / KPR


Mass: 32212.980 Da / Num. of mol.: 1 / Fragment: MytuD.18678.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2573, MT2649, MTCY227.28c / Production host: Escherichia coli (E. coli)
References: UniProt: Q50648, UniProt: P9WIL1*PLUS, 2-dehydropantoate 2-reductase

-
Non-polymers , 6 types, 288 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein incubated with 4mM NADP for ~5min, then added 1 to 1 with Morpheus(g5): 10% PEG-20,0000, 20% PEG-MME-550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each sodium formate, ammonium acetate, ...Details: Protein incubated with 4mM NADP for ~5min, then added 1 to 1 with Morpheus(g5): 10% PEG-20,0000, 20% PEG-MME-550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartarate, sodium oxamate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→55.5 Å / Num. all: 29148 / Num. obs: 29066 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 25.385 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.5373.4113966214699.9
1.9-1.950.4364.28132852051100
1.95-2.010.3435.27129531998100
2.01-2.070.2796.44126291944100
2.07-2.140.2257.7812360190799.9
2.14-2.210.1918.97119201834100
2.21-2.290.1819.8411442178199.8
2.29-2.390.14611.7311051170799.8
2.39-2.490.12413.410759165899.9
2.49-2.620.11414.6610049155799.9
2.62-2.760.116.289733150999.9
2.76-2.930.08718.429092142099.6
2.93-3.130.0721.568460133499.9
3.13-3.380.0625.247904126899.5
3.38-3.70.05528.526959114099.1
3.7-4.140.04930.216305103999
4.14-4.780.04631.45563395499.4
4.78-5.850.04430.3486480699.1
5.85-8.270.04229.67382163298.6
8.270.03333.55207338197.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G17

3g17


Resolution: 1.85→55.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1665 / WRfactor Rwork: 0.1342 / FOM work R set: 0.8908 / SU B: 3.973 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1053 / SU Rfree: 0.1011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 1475 5.1 %RANDOM
Rwork0.1458 ---
obs0.1473 29066 99.7 %-
all-30541 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.15 Å2 / Biso mean: 20.119 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2---1.04 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 65 283 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192315
X-RAY DIFFRACTIONr_bond_other_d0.0010.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.4962.0013181
X-RAY DIFFRACTIONr_angle_other_deg0.78835111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65722.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
X-RAY DIFFRACTIONr_mcbond_it0.8221.1231208
X-RAY DIFFRACTIONr_mcbond_other0.8221.1211206
X-RAY DIFFRACTIONr_mcangle_it1.3851.6761514
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 123 -
Rwork0.194 2017 -
all-2140 -
obs--99.72 %
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)
11.2968-0.1548-0.17621.2013-0.26811.2408-0.02130.0831-0.0433-0.0804-0.0024-0.0861-0.00780.0780.02370.0479-0.01660.01910.06250.00120.041956.726216.2592-11.3791
21.2911-0.05550.07750.5445-0.16841.1429-0.0338-0.0567-0.06480.00780.0076-0.07850.01760.01110.02620.0513-0.0088-0.00460.04170.00240.058754.152415.274-1.2615
30.46530.2299-0.18910.4228-0.20670.32790.0206-0.07440.00870.0037-0.03840.0212-0.05370.04170.01780.0718-0.0119-0.00850.0688-0.00110.05343.280417.02349.195
40.64990.01290.05680.72260.12170.7325-0.04160.0023-0.05560.0133-0.0006-0.06020.0050.00980.04220.0545-0.0102-0.0030.05710.00590.049639.78976.78017.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 87
2X-RAY DIFFRACTION2A88 - 140
3X-RAY DIFFRACTION3A141 - 225
4X-RAY DIFFRACTION4A226 - 295

+
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