[English] 日本語
Yorodumi
- PDB-2xxj: Penta mutant of lactate dehydrogenase from Thermus thermophilus, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xxj
TitlePenta mutant of lactate dehydrogenase from Thermus thermophilus, ternary complex
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HYPERTHERMOPHILE
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.964 Å
AuthorsTickle, J. / de Mendoza Barbera, E. / Vellieux, F.M.D.
CitationJournal: To be Published
Title: Lactate Dehydrogenase from T. Thermophilus, Penta- Mutant (Ternary Complex)
Authors: Tickle, J. / De Mendoza Barbera, E. / Vellieux, F.M.D.
History
DepositionNov 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
C: L-LACTATE DEHYDROGENASE
D: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,09510
Polymers130,3974
Non-polymers1,6976
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-127.2 kcal/mol
Surface area41920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.150, 147.360, 152.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
L-LACTATE DEHYDROGENASE / L-LDH


Mass: 32599.373 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DH5ALPHA / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.46 Å3/Da / Density % sol: 49.97 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M NACACODYLATE 0.2M NAAC PH 6.5, 15% W/V PEG 8000. DROPLETS = 2.0 MICROL PROTEIN, 2 MICROL PRECIPITANT, 0.5 MICROL ADDITIVE (30% D(PLUS)-GLUCOSE MONOHYDRATE).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97245
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 31, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97245 Å / Relative weight: 1
ReflectionResolution: 1.96→105.9 Å / Num. obs: 91523 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.37 % / Biso Wilson estimate: 25.04 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.94
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 4.91 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.32 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7P
Resolution: 1.964→67.644 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 4577 5 %
Rwork0.1752 --
obs0.1777 91516 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.659 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 29.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.0938 Å20 Å20 Å2
2---4.0562 Å20 Å2
3----0.0376 Å2
Refinement stepCycle: LAST / Resolution: 1.964→67.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9175 0 110 643 9928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079541
X-RAY DIFFRACTIONf_angle_d1.13713038
X-RAY DIFFRACTIONf_dihedral_angle_d16.3173523
X-RAY DIFFRACTIONf_chiral_restr0.1071540
X-RAY DIFFRACTIONf_plane_restr0.0051685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9643-2.03460.28314260.24247711X-RAY DIFFRACTION89
2.0346-2.1160.28554730.20498694X-RAY DIFFRACTION100
2.116-2.21230.25734790.18848648X-RAY DIFFRACTION100
2.2123-2.3290.25864310.18158726X-RAY DIFFRACTION100
2.329-2.47490.24744400.17478751X-RAY DIFFRACTION100
2.4749-2.6660.22824480.17048741X-RAY DIFFRACTION100
2.666-2.93430.23714310.18248797X-RAY DIFFRACTION100
2.9343-3.35890.23494750.1838830X-RAY DIFFRACTION100
3.3589-4.23170.20174480.15988900X-RAY DIFFRACTION100
4.2317-67.68410.18715260.1499141X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4505-0.3345-0.01660.45270.11160.4176-0.00520.00530.0950.11160.0063-0.0952-0.04920.08270.00390.0302-0.0011-0.01370.04380.02420.129817.857424.666831.6706
20.75840.0708-0.06660.23180.54751.3924-0.03710.03650.2159-0.25660.0660.1456-0.68270.076-0.02710.3735-0.0349-0.00480.12150.09410.356920.215836.916615.6662
30.29630.1923-0.2170.41170.03310.29660.09330.1523-0.0446-0.1689-0.09040.0022-0.0185-0.1115-0.01570.0701-0.03280.02790.06150.1028-0.011311.506715.29888.5023
40.1198-0.0475-0.19350.32560.09160.3118-0.0180.1335-0.0104-0.1343-0.08060.0584-0.1539-0.29060.05940.21370.0574-0.03220.35280.04960.1331-4.59179.89010.7421
50.52950.4219-0.3310.3354-0.2630.20650.2130.37080.144-0.1588-0.3207-0.015-0.1873-0.05520.08480.39350.1027-0.11250.26110.07430.2153-2.105926.506811.407
60.8732-0.1748-0.17350.7241-0.4810.38630.06580.05670.052-0.053-0.0414-0.06010.07280.1250.04880.0867-0.02140.01440.11160.03640.058217.809716.038310.7599
70.64240.645-0.0711.7237-0.50640.189-0.05670.44690.0266-0.37370.06250.08750.1089-0.0576-0.09980.17720.01940.1190.11080.3396-0.122416.425425.3643-3.3312
80.22350.3416-0.17140.5508-0.34940.5644-0.0440.09560.0231-0.12850.08190.08630.0779-0.0694-0.05620.0597-0.0181-0.03910.09370.05120.0802-3.213818.324626.1018
90.0604-0.0855-0.12830.6233-0.31820.5638-0.03780.04680.04170.01130.14750.2388-0.0258-0.1861-0.10970.0210.0081-0.00650.07950.07040.1619-12.026924.509840.3698
100.0095-0.00390.01060.8775-0.2670.095-0.0132-0.0302-0.00730.0530.0407-0.1569-0.0635-0.0337-0.00270.070.0009-0.01240.040.02810.089212.675920.17452.3466
110.6324-0.49240.20990.8338-0.57620.4481-0.12720.06240.2510.2797-0.0651-0.469-0.18550.03150.13060.214-0.0259-0.07780.1080.04690.354323.44325.22456.566
120.5777-0.41030.42880.3017-0.17381.405-0.05370.02570.18670.1339-0.097-0.1803-0.41230.03090.14140.104-0.0118-0.0020.0190.02960.18929.48233.597346.4862
130.2053-0.030.0040.8285-0.07830.28480.04560.0166-0.02690.1340.06150.00360.0721-0.0136-0.07290.03640.0036-0.00460.03620.04160.0673-2.102717.515449.9165
140.2097-0.16090.01590.32841.17356.64180.0278-0.0815-0.01380.1092-0.0887-0.0172-0.2588-0.52420.04410.13290.0270.05020.06860.0260.1031-7.131630.983859.5173
150.3183-0.1624-0.04190.19470.10420.5234-0.04980.06630.00570.0150.0183-0.03960.01450.05450.02110.0803-0.01570.01890.078-0.00620.071826.1123-7.177327.8694
160.5195-0.3963-0.24360.30980.15050.8582-0.1225-0.0618-0.11560.16280.15280.07420.4190.1626-0.00160.29590.09660.01140.13050.0130.163534.8902-20.800145.4568
170.5173-0.1766-0.31830.21830.26030.5669-0.08480.03380.12170.08920.0993-0.05170.15710.0207-0.01040.05130.0141-0.0170.02870.01540.051621.2889-1.696650.3001
181.4047-0.6651-0.39672.1484-0.42850.7227-0.06670.0027-0.14150.14020.1352-0.00770.2939-0.01880.00220.1222-0.029-0.0050.00470.03040.04125.9174-6.812260.5258
190.6867-0.2557-0.08570.35110.50250.84980.01360.0666-0.10780.30120.0240.06330.22670.1285-0.04690.1370.006200.0507-0.00320.054517.962-9.266841.5943
200.434-0.2360.00390.9399-0.2380.1808-0.0139-0.04640.19110.13650.0421-0.0609-0.01110.03360.02430.0542-0.0057-0.01740.0449-0.03520.006927.20723.864153.3873
210.9146-0.50790.44931.024-0.61830.4897-0.0156-0.2670.0240.4084-0.06370.00080.06920.11770.02060.22330.0524-0.06680.13990.02270.068130.4314-7.876562.2301
220.40010.03070.05990.54060.01180.21530.0057-0.01870.08340.3098-0.06670.1684-0.0028-0.00450.04420.1235-0.02230.07520.0476-0.01970.0753.4927-13.48235.9376
230.45830.35020.20360.43490.00890.21940.02840.3133-0.1252-0.00640.0062-0.08760.02860.1949-0.06690.10830.00080.04780.2412-0.04850.208915.1559-29.675221.4131
240.47320.05120.17170.5685-0.27850.1146-0.04170.2001-0.0255-0.09570.08140.10470.05980.0308-0.02180.0526-0.03110.0510.0999-0.03050.03596.3401-16.233115.1941
250.5890.0851-0.4310.3907-0.33210.5071-0.08820.24850.0369-0.1246-0.0014-0.08360.1266-0.28420.03640.2206-0.02310.09540.20930.02680.179126.1007-3.37281.4627
260.22720.2983-0.28811.1228-0.5540.4067-0.05160.0169-0.0373-0.12110.0334-0.15440.0525-0.09970.0380.1156-0.0230.04950.1592-0.05850.124922.1811-19.050713.3873
270.70820.2170.31931.04370.27330.1572-0.10050.2453-0.0527-0.09970.0540.1293-0.12320.03830.04190.0548-0.04610.03680.1486-0.01220.01232.527-11.768513.4841
280.73050.40410.25081.35551.3691.417-0.10380.4408-0.241-0.19630.2719-0.14920.05990.2023-0.14460.1081-0.07540.01410.0987-0.2237-0.05184.3316-25.09813.2606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:74)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 75:108)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 109:194)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 195:213)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 214:222)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 223:288)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 289:310)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:57)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 58:141)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 142:194)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 195:208)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 209:222)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 223:290)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 291:309)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 1:75)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 76:99)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 100:194)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 195:217)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 218:243)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 244:288)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 289:310)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 1:75)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 76:83)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 84:189)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 190:206)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 207:222)
27X-RAY DIFFRACTION27(CHAIN D AND RESID 223:288)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 289:310)

+
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