[English] 日本語
Yorodumi
- PDB-4f3y: X-Ray Crystal Structure of Dihydrodipicolinate reductase from Bur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f3y
TitleX-Ray Crystal Structure of Dihydrodipicolinate reductase from Burkholderia thailandensis
ComponentsDihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Dihydrodipicolinate reductase / NAD/NADH
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 / NAD binding / NADP 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
4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_special_symmetry / 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_auth_seq_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_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
Revision 1.3Oct 22, 2025Group: Derived calculations / Structure summary
Category: audit_author / entity ...audit_author / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23117
Polymers57,0912
Non-polymers14015
Water4,774265
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,46234
Polymers114,1824
Non-polymers28030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area14170 Å2
ΔGint-138 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.740, 158.370, 70.440
Angle α, β, γ (deg.)90.00, 130.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-489-

HOH

DetailsUNKNOWN

-
Components

#1: Protein Dihydrodipicolinate reductase / DHPR


Mass: 28545.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I1208, dapB / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SZ94, EC: 1.3.1.26
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06M Magnesium chloride, 0.06M Calcium chloride, 0.10M Imidazole, 0.10M MES, 30% PEG550MME, 30% PEG20,000, ButhA.00820.a PW.33405 28.89mg/ml, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 34301 / Num. obs: 33386 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 34.431 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.3576.01153932401195.3
2.15-2.210.4695.07168332277192
2.21-2.280.22411.47172592321196.2
2.28-2.350.278.52161812155192.4
2.35-2.420.20310.92164992183198.2
2.42-2.510.16712.99163242157198.4
2.51-2.60.15313.64158052081198.5
2.6-2.710.13815.32150081979198.3
2.71-2.830.10119.66146741928199
2.83-2.970.08322.37140461847198.9
2.97-3.130.06727.1133401747198.9
3.13-3.320.04835.55126821663198.8
3.32-3.550.03942.94117961547199.1
3.55-3.830.03651.51110341463199.1
3.83-4.20.0356.76101931339199
4.2-4.70.02764.4793031223198.7
4.7-5.420.02860.9382441077198.8
5.42-6.640.03155.066898901198.8
6.64-9.390.02369.985296701198.7
9.39-500.02184.282858396195.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ARZ

1arz


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.66 / SU ML: 0.133 / Isotropic thermal model: Isotropic/TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1688 5.1 %RANDOM
Rwork0.1898 ---
all0.1922 34301 --
obs0.1922 33385 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 32.053 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å21.87 Å2
2---1.27 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 15 265 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193978
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9585387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56222.901162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3931535
X-RAY DIFFRACTIONr_chiral_restr0.0910.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023010
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 136 -
Rwork0.207 2241 -
all-2377 -
obs-2401 95.89 %
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)
13.4954-0.3132-0.27044.6217-3.10824.6872-0.0249-0.0323-0.10610.10160.38310.74870.1753-0.42-0.35820.0699-0.02740.0720.05240.03250.1723-50.9165-39.545617.801
22.4268-0.0534-0.19595.2274-2.53462.8132-0.0077-0.0444-0.15830.2991-0.2577-0.40610.03460.2260.26540.10390.01150.0010.06160.02250.0507-37.2129-37.564116.4052
30.93250.3774-0.50812.46360.0441.49260.0115-0.13890.0296-0.1659-0.0156-0.59360.07480.42590.00410.04310.03640.0410.1340.01330.1885-40.4888-8.280623.7336
40.86350.353-0.81342.8079-0.07161.36820.0447-0.1781-0.02410.0584-0.0391-0.53570.03480.3245-0.00560.01570.0032-0.00290.1007-0.0170.1367-44.6336-3.75729.6911
52.4971-1.2123-3.23113.9749-1.2967.450.22380.00230.1833-0.0978-0.08570.1344-0.28240.1405-0.13810.0670.00250.02120.01580.01580.1244-41.1886-25.050310.4094
63.4406-1.3355-1.40385.33430.58994.2437-0.1401-0.02530.20770.26910.20330.2967-0.015-0.1935-0.06320.08010.01770.05280.020.01880.1225-48.181829.116718.9392
72.39821.0689-1.34214.34541.814.57940.2308-0.03520.63230.0380.06370.2795-0.6786-0.0165-0.29450.14620.02510.07710.03810.03740.2626-46.636135.261417.4164
84.5261-0.9373-2.31966.39591.06265.2943-0.08860.8039-0.0083-1.01780.13520.91160.1723-1.1356-0.04670.2471-0.0564-0.12790.34760.1110.1931-51.141924.86113.1327
90.7286-0.0707-0.45752.47560.39481.51240.07030.23530.1053-0.5418-0.00650.0939-0.0985-0.1989-0.06380.12640.0168-0.01450.07910.03660.0333-59.856-3.826612.0865
106.53281.8353-4.34713.4936-2.3844.5633-0.44380.3674-0.2427-0.4010.19440.06230.6778-0.27730.24940.2046-0.05760.06740.0322-0.01770.0472-44.168215.04038.091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 51
2X-RAY DIFFRACTION2A52 - 124
3X-RAY DIFFRACTION3A125 - 184
4X-RAY DIFFRACTION4A185 - 236
5X-RAY DIFFRACTION5A237 - 268
6X-RAY DIFFRACTION6B2 - 45
7X-RAY DIFFRACTION7B46 - 71
8X-RAY DIFFRACTION8B72 - 125
9X-RAY DIFFRACTION9B126 - 236
10X-RAY DIFFRACTION10B237 - 268

+
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