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- PDB-2jht: CRYSTAL STRUCTURE OF RHOGDI K135T,K138T,K141T MUTANT -

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Entry
Database: PDB / ID: 2jht
TitleCRYSTAL STRUCTURE OF RHOGDI K135T,K138T,K141T MUTANT
ComponentsRHO GDP-DISSOCIATION INHIBITOR 1
KeywordsINHIBITOR / SURFACE ENTROPY REDUCTION / GTPASE ACTIVATION / CRYSTAL ENGINEERING
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of synaptic vesicle cycle / regulation of Rho protein signal transduction / RHOC GTPase cycle / Rho protein signal transduction / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / RHOH GTPase cycle ...Rho GDP-dissociation inhibitor activity / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of synaptic vesicle cycle / regulation of Rho protein signal transduction / RHOC GTPase cycle / Rho protein signal transduction / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / RHOH GTPase cycle / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / Schaffer collateral - CA1 synapse / regulation of protein localization / cytoskeleton / negative regulation of apoptotic process / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
: / Rho GDP-dissociation inhibitor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCooper, D.R. / Grelewska, K. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Protein Crystallization by Surface Entropy Reduction: Optimization of the Ser Strategy
Authors: Cooper, D.R. / Boczek, T. / Grelewska, K. / Pinkowska, M. / Sikorska, M. / Zawadzki, M. / Derewenda, Z.S.
History
DepositionFeb 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHO GDP-DISSOCIATION INHIBITOR 1
B: RHO GDP-DISSOCIATION INHIBITOR 1
C: RHO GDP-DISSOCIATION INHIBITOR 1
D: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0467
Polymers62,8474
Non-polymers1993
Water4,630257
1
A: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8153
Polymers15,7121
Non-polymers1032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8082
Polymers15,7121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)15,7121
Polymers15,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)15,7121
Polymers15,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)190.832, 34.022, 103.940
Angle α, β, γ (deg.)90.00, 115.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
RHO GDP-DISSOCIATION INHIBITOR 1 / RHO GDI 1 / RHO-GDI ALPHA


Mass: 15711.820 Da / Num. of mol.: 4 / Fragment: ISOPRENYL-BINDING DOMAIN, RESIDUES 66-201 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52565
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 134 TO THR ENGINEERED RESIDUE IN CHAIN A, LYS 137 TO THR ...ENGINEERED RESIDUE IN CHAIN A, LYS 134 TO THR ENGINEERED RESIDUE IN CHAIN A, LYS 137 TO THR ENGINEERED RESIDUE IN CHAIN A, LYS 140 TO THR ENGINEERED RESIDUE IN CHAIN B, LYS 134 TO THR ENGINEERED RESIDUE IN CHAIN B, LYS 137 TO THR ENGINEERED RESIDUE IN CHAIN B, LYS 140 TO THR ENGINEERED RESIDUE IN CHAIN C, LYS 134 TO THR ENGINEERED RESIDUE IN CHAIN C, LYS 137 TO THR ENGINEERED RESIDUE IN CHAIN C, LYS 140 TO THR ENGINEERED RESIDUE IN CHAIN D, LYS 134 TO THR ENGINEERED RESIDUE IN CHAIN D, LYS 137 TO THR ENGINEERED RESIDUE IN CHAIN D, LYS 140 TO THR
Sequence detailsMUTATIONS ENGINEERED TO FACILITATE CRYSTALLIZATION

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 8.5
Details: 35% PEG 4000 0.2 M LITHIUM SULFATE 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 44864 / % possible obs: 91.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.6 / % possible all: 64.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BXW

2bxw


Resolution: 1.88→93.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.582 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1143 2.5 %RANDOM
Rwork0.222 ---
obs0.223 43701 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-1.86 Å2
2--3.95 Å20 Å2
3----4.27 Å2
Refinement stepCycle: LAST / Resolution: 1.88→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 11 257 4682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9666158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66323.641195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38415807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4121528
X-RAY DIFFRACTIONr_chiral_restr0.1380.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.21778
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23018
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2161.52831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82824488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94931987
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3274.51669
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 50
Rwork0.251 1850
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)
10.4290.1449-0.00770.93650.22052.25110.0360.1241-0.02920.12990.036-0.00890.0113-0.2039-0.072-0.0196-0.026-0.0039-0.0703-0.0158-0.04435.6063-6.58156.9263
22.1714-0.85621.29890.4539-0.00925.367-0.05280.6096-0.08470.1303-0.0348-0.0205-0.35440.22810.0876-0.0015-0.06120.01150.0304-0.0199-0.11538.6518-6.880753.5845
31.6385-0.2123-1.45980.3524-0.335.97720.04210.30760.14390.01-0.0624-0.03570.2472-0.39720.0202-0.1427-0.0566-0.00270.19510.0026-0.19726.0575-11.1818-29.2509
41.41510.3783-2.48030.43990.39447.64860.11420.37120.05440.1929-0.0835-0.36480.3556-0.9099-0.0307-0.1326-0.08140.0160.49060.042-0.35954.4645-11.673116.7856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A65 - 202
2X-RAY DIFFRACTION2B65 - 202
3X-RAY DIFFRACTION3C65 - 202
4X-RAY DIFFRACTION4D65 - 202

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