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- PDB-1dce: CRYSTAL STRUCTURE OF RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN -

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Basic information

Entry
Database: PDB / ID: 1dce
TitleCRYSTAL STRUCTURE OF RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN
Components
  • PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
  • PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
KeywordsTRANSFERASE / RAB GERANYLGERANYLTRANSFERASE / 2.0 A RESOLUTION / N-FORMYLMETHIONINE / ALPHA SUBUNIT / BETA SUBUNIT
Function / homology
Function and homology information


isoprenoid binding / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protein geranylgeranyltransferase type II / RAB geranylgeranylation / Rab-protein geranylgeranyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / small GTPase binding / zinc ion binding / cytoplasm
Similarity search - Function
Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / Rab geranylgeranyltransferase alpha-subunit, insert domain / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. ...Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / Rab geranylgeranyltransferase alpha-subunit, insert domain / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Geranylgeranyl transferase type-2 subunit alpha / Geranylgeranyl transferase type-2 subunit beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsZhang, H. / Seabra, M.C. / Deisenhofer, H.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of Rab geranylgeranyltransferase at 2.0 A resolution.
Authors: Zhang, H. / Seabra, M.C. / Deisenhofer, J.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
B: PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
C: PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
D: PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,9336
Polymers203,8034
Non-polymers1312
Water14,934829
1
A: PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
B: PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9673
Polymers101,9012
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-67 kcal/mol
Surface area37500 Å2
MethodPISA
2
C: PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
D: PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9673
Polymers101,9012
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-67 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.864, 77.439, 121.775
Angle α, β, γ (deg.)74.60, 79.91, 67.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)


Mass: 65009.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: Q08602, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)


Mass: 36892.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: Q08603, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 40 %
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
30.25 Mmagnesium acetate1reservoir
410 mMsodium phosphate1reservoir
56 %ethylene glycol1reservoir
617-21 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeID
ROTATING ANODERIGAKU RU3001
SYNCHROTRONAPS 19-ID2
Detector
TypeIDDetector
RIGAKU RAXIS II1IMAGE PLATE
CUSTOM-MADE2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 446152 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.683 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.33 / % possible all: 86.1
Reflection
*PLUS
Num. obs: 118808 / Num. measured all: 446152
Reflection shell
*PLUS
% possible obs: 86.1 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Cross valid method: FREE-R / σ(F): 0 / σ(I): -3 / ESU R: 0.25608 / ESU R Free: 0.21363
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 5991 5 %RANDOM
Rwork0.2147 ---
all-127139 --
obs-118808 93.4 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14266 0 2 829 15097
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 53 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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