[English] 日本語
Yorodumi
- PDB-1dru: ESCHERICHIA COLI DHPR/NADH COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dru
TitleESCHERICHIA COLI DHPR/NADH COMPLEX
ComponentsDIHYDRODIPICOLINATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / amino acid biosynthetic process / NAD binding / NADP binding / identical protein binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReddy, S.G. / Scapin, G. / Blanchard, J.S.
Citation
Journal: Biochemistry / Year: 1996
Title: Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes.
Authors: Reddy, S.G. / Scapin, G. / Blanchard, J.S.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Scapin, G. / Blanchard, J.S. / Sacchettini, J.C.
#2: Journal: Biochemistry / Year: 1995
Title: Expression, Purification, and Characterization of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Reddy, S.G. / Sacchettini, J.C. / Blanchard, J.S.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4572
Polymers28,7941
Non-polymers6631
Water1,13563
1
A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8288
Polymers115,1754
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area16180 Å2
ΔGint-63 kcal/mol
Surface area40390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.200, 84.500, 91.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein DIHYDRODIPICOLINATE REDUCTASE / DHPR / DAPB


Mass: 28793.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAPB / Plasmid: PET3D / Gene (production host): DAPB / Production host: Escherichia coli (E. coli) / Strain (production host): BL213D / References: UniProt: P04036, EC: 1.3.1.26
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.74 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Scapin, G., (1995) Biochemistry, 34, 3502.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium salfate1reservoir
2100 mMHEPES1reservoirpH7.5
318 mg/mlprotein1drop
42.2 Mammonium salfate1drop
5100 mMHEPES1drop
61.5-2.0 MNADPH1drop

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19014 / % possible obs: 77.1 % / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.54 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.296 / % possible all: 39.3
Reflection
*PLUS
Rmerge(I) obs: 0.076

-
Processing

Software
NameClassification
AMoREphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DHPR-NADPH

Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL.DAT / σ(F): 2
Stereochemistry target values: ENGH AND HUBER MODIFIED FOR TNT
RfactorNum. reflection% reflection
obs0.192 13953 85 %
Solvent computationBsol: 693.6 Å2 / ksol: 1.22 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 44 63 2081
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01920813.5
X-RAY DIFFRACTIONt_angle_deg2.527662.5
X-RAY DIFFRACTIONt_dihedral_angle_d2012570
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.026493
X-RAY DIFFRACTIONt_gen_planes0.0293097
X-RAY DIFFRACTIONt_it4.43120810.4
X-RAY DIFFRACTIONt_nbd0.0911110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 14276 / Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg200
X-RAY DIFFRACTIONt_planar_d0.0263
X-RAY DIFFRACTIONt_plane_restr0.0297

+
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