[English] 日本語
Yorodumi
- PDB-3p2y: Crystal structure of alanine dehydrogenase/pyridine nucleotide tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p2y
TitleCrystal structure of alanine dehydrogenase/pyridine nucleotide transhydrogenase from Mycobacterium smegmatis
ComponentsAlanine dehydrogenase/pyridine nucleotide transhydrogenase
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / non-pathogenic species / ortholog / dehydrogenase / pyruvate
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / metal ion binding / plasma membrane
Similarity search - Function
Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8977
Polymers39,6301
Non-polymers2676
Water6,774376
1
A: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules

A: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,79414
Polymers79,2602
Non-polymers53512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5190 Å2
ΔGint-57 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.760, 89.760, 179.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-361-

CA

21A-701-

HOH

-
Components

#1: Protein Alanine dehydrogenase/pyridine nucleotide transhydrogenase


Mass: 39629.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0152 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QNT0, alanine dehydrogenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, ...Details: 21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 38305 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 23.517 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 42.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.82-1.8714.10.23411.1325622842230981.2
1.87-1.920.20213.739524265195.8
1.92-1.970.16918.346694265598.8
1.97-2.030.13921.846885258499
2.03-2.10.12324.845738253899.2
2.1-2.180.10228.943881242199.1
2.18-2.260.08932.942528236599.3
2.26-2.350.07438.241053227699.3
2.35-2.450.06742.239144218199.5
2.45-2.570.06145.638013211899.4
2.57-2.710.05549.535640199699.6
2.71-2.880.04855.134052191899.7
2.88-3.080.04459.631970180399.7
3.08-3.320.03867.329724169399.8
3.32-3.640.03675.126994156199.9
3.64-4.070.03479.524373143199.9
4.07-4.70.03282.621750129099.9
4.7-5.760.03180.517938110099.9
5.76-8.140.02980.714452878100
8.140.02683.8786253798.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.89 Å
Translation3 Å44.89 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L7D

1l7d


Resolution: 1.82→40.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1922 / WRfactor Rwork: 0.1606 / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8996 / SU B: 3.89 / SU ML: 0.057 / SU R Cruickshank DPI: 0.1061 / SU Rfree: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1913 5 %RANDOM
Rwork0.165 ---
obs0.1665 38192 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.05 Å2 / Biso mean: 19.0145 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 12 376 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222593
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9863570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04424.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0381517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211939
X-RAY DIFFRACTIONr_mcbond_it0.8451.51764
X-RAY DIFFRACTIONr_mcangle_it1.50922849
X-RAY DIFFRACTIONr_scbond_it2.4143829
X-RAY DIFFRACTIONr_scangle_it4.2254.5705
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 108 -
Rwork0.202 2186 -
all-2294 -
obs--80.8 %
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)
10.5457-0.0021-0.06870.4315-0.01370.50170.04330.0116-0.0873-0.04540.0106-0.0443-0.05470.0066-0.05390.0137-0.00210.00310.06680.02510.044466.153339.4878-13.0551
20.0119-0.00050.04380.1665-0.03430.40340.0073-0.00130.01290.00470.0103-0.0265-0.0506-0.0577-0.01760.0272-0.00160.01770.06670.04090.054257.003649.8573-4.3285
30.9893-0.03240.22520.2869-0.19080.3359-0.0244-0.02340.11040.05120.01430.0209-0.0578-0.05180.01010.0372-0.004-0.00150.04260.00820.041949.002747.56818.8239
40.1950.18470.12670.4772-0.24980.54730.01440.02550.0518-0.02840.01340.08320.0669-0.0043-0.02780.0087-0.0058-0.0060.08470.05170.043753.256446.1756-12.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 71
2X-RAY DIFFRACTION2A72 - 152
3X-RAY DIFFRACTION3A153 - 306
4X-RAY DIFFRACTION4A307 - 356

+
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