[English] 日本語
Yorodumi
- PDB-4l04: Crystal Structure Analysis of human IDH1 mutants in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l04
TitleCrystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / cytosolic
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / glutathione metabolic process / tricarboxylic acid cycle / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsConcha, N.O. / Smallwood, A.M.
CitationJournal: Biochemistry / Year: 2013
Title: Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism.
Authors: Rendina, A.R. / Pietrak, B. / Smallwood, A. / Zhao, H. / Qi, H. / Quinn, C. / Adams, N.D. / Concha, N. / Duraiswami, C. / Thrall, S.H. / Sweitzer, S. / Schwartz, B.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_conn.ptnr2_label_seq_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: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
E: Isocitrate dehydrogenase [NADP] cytoplasmic
F: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,84824
Polymers289,2716
Non-polymers5,57718
Water1,24369
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2838
Polymers96,4242
Non-polymers1,8596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-75 kcal/mol
Surface area30560 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2838
Polymers96,4242
Non-polymers1,8596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-71 kcal/mol
Surface area30530 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NADP] cytoplasmic
F: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2838
Polymers96,4242
Non-polymers1,8596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-75 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.410, 116.622, 275.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 48211.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.9
Details: 16-20% PEG MME 2000, 100mM MES, pH 6.9, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.866→50 Å / Num. obs: 70831 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 71.28 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.866-36.30.631196.5
3-3.126.30.46197.6
3.12-3.276.30.343198.3
3.27-3.446.30.252199.4
3.44-3.656.30.191199.6
3.65-3.946.40.148199.7
3.94-4.336.30.115199.8
4.33-4.966.20.102199.6
4.96-6.246.80.104199.9
6.24-506.80.089199.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→49.24 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.8953 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 3578 5.06 %RANDOM
Rwork0.1999 ---
obs0.2028 70733 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.11 Å2
Baniso -1Baniso -2Baniso -3
1--5.8108 Å20 Å20 Å2
2---1.9674 Å20 Å2
3---7.7782 Å2
Refine analyzeLuzzati coordinate error obs: 0.483 Å
Refinement stepCycle: LAST / Resolution: 2.87→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19199 0 354 69 19622
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00919997HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1427106HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7002SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes502HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2895HARMONIC5
X-RAY DIFFRACTIONt_it19997HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.87→2.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3043 226 4.98 %
Rwork0.2381 4313 -
all0.2415 4539 -
obs--98.3 %
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)
10-0.1238-0.262300.26180.42490.0401-0.02240.0474-0.01250.1856-0.10640.14380.1608-0.22570.31970.0215-0.06740.03-0.0547-0.12678.862-48.653-98.2878
22.6178-1.4635-0.05172.23340.07311.09230.263-0.0025-0.7908-0.16120.00180.66220.38910.3684-0.2648-0.23120.1233-0.2071-0.1447-0.18390.050320.6685-44.7945-69.4636
32.05750.09560.38281.67370.09191.08060.10280.04550.1301-0.03250.07020.1756-0.1780.4242-0.173-0.2057-0.02660.0855-0.0025-0.163-0.109821.0931-13.9543-67.0476
40.60560.24130.03931.9150.05432.027-0.10040.1072-0.0232-0.84840.2071-0.5040.2059-0.0007-0.10680.219-0.06330.2626-0.1621-0.0029-0.1218-23.7184-47.6629-110.655
50.20820.23330.09822.7028-0.83492.2614-0.02270.05380.1395-0.58080.0683-0.2888-0.593-0.3157-0.04550.33170.14960.2148-0.15260.0002-0.1581-27.1869-17.2212-106.64
60.71520.34350.04981.9826-0.24891.8283-0.09260.10710.1632-0.78740.2370.5412-0.22660.0006-0.14440.269-0.0086-0.2962-0.2098-0.0386-0.090925.9117-68.9448-112.268
70.35360.485-0.49192.05850.40072.4294-0.02540.0358-0.1044-0.6470.03420.19160.61840.2384-0.00890.37810.2198-0.2487-0.1521-0.0577-0.203528.3992-99.4718-107.952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }A504
2X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }C503
3X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }B502
4X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }E503
5X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }D503
6X-RAY DIFFRACTION1{ A|504 - A|504 C|503 - C|503 B|502 - B|502 E|503 - E|503 D|503 - D|503 F|503 - F|503 }F503
7X-RAY DIFFRACTION2{ A|5 - A|415 }A5 - 415
8X-RAY DIFFRACTION3{ B|3 - B|414 }B3 - 414
9X-RAY DIFFRACTION4{ C|4 - C|415 }C4 - 415
10X-RAY DIFFRACTION5{ D|3 - D|414 }D3 - 414
11X-RAY DIFFRACTION6{ E|4 - E|415 }E4 - 415
12X-RAY DIFFRACTION7{ F|3 - F|414 }F3 - 414

+
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