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- PDB-2ov2: The crystal structure of the human RAC3 in complex with the CRIB ... -

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Basic information

Entry
Database: PDB / ID: 2ov2
TitleThe crystal structure of the human RAC3 in complex with the CRIB domain of human p21-activated kinase 4 (PAK4)
Components
  • Ras-related C3 botulinum toxin substrate 3
  • Serine/threonine-protein kinase PAK 4
KeywordsPROTEIN BINDING/TRANSFERASE / GTPase RAC3 / small GTP binding protein / p21 rac / ras-related C3 botulinum toxin substrate 3 / signalling protein / CRIB / kinase / Structural Genomics / Structural Genomics Consortium / SGC / PROTEIN BINDING-TRANSFERASE COMPLEX
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / dendritic spine development / cadherin binding involved in cell-cell adhesion / respiratory burst / cortical cytoskeleton organization / cell projection assembly ...cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / dendritic spine development / cadherin binding involved in cell-cell adhesion / respiratory burst / cortical cytoskeleton organization / cell projection assembly / motor neuron axon guidance / PCP/CE pathway / Activation of RAC1 / positive regulation of cell adhesion mediated by integrin / synaptic transmission, GABAergic / RHOV GTPase cycle / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Rac protein signal transduction / RHOQ GTPase cycle / filamentous actin / : / regulation of MAPK cascade / RHOU GTPase cycle / neuromuscular process controlling balance / CDC42 GTPase cycle / regulation of postsynapse assembly / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / homeostasis of number of cells within a tissue / cytoskeleton organization / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / endomembrane system / cellular response to starvation / small monomeric GTPase / actin filament organization / cell periphery / cell chemotaxis / adherens junction / regulation of actin cytoskeleton organization / regulation of cell growth / Wnt signaling pathway / positive regulation of angiogenesis / calcium-dependent protein binding / cell migration / lamellipodium / regulation of cell shape / G protein activity / actin cytoskeleton organization / growth cone / cytoplasmic vesicle / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein kinase activity / neuron projection / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / neuronal cell body / GTPase activity / apoptotic process / endoplasmic reticulum membrane / protein kinase binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / signal transduction / extracellular exosome / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Serine/threonine-protein kinase PAK 4 / Ras-related C3 botulinum toxin substrate 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUgochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Bunkoczi, G. / Debreczeni, J.E.D. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Ugochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Bunkoczi, G. / Debreczeni, J.E.D. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the human RAC3 in complex with the CRIB domain of human p21-activated kinase 4 (PAK4)
Authors: Ugochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Knapp, S. / Doyle, D.A.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / struct_conn / struct_ncs_dom_lim / 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 3
F: Ras-related C3 botulinum toxin substrate 3
B: Ras-related C3 botulinum toxin substrate 3
C: Ras-related C3 botulinum toxin substrate 3
G: Ras-related C3 botulinum toxin substrate 3
D: Ras-related C3 botulinum toxin substrate 3
E: Ras-related C3 botulinum toxin substrate 3
H: Ras-related C3 botulinum toxin substrate 3
I: Serine/threonine-protein kinase PAK 4
J: Serine/threonine-protein kinase PAK 4
K: Serine/threonine-protein kinase PAK 4
L: Serine/threonine-protein kinase PAK 4
M: Serine/threonine-protein kinase PAK 4
N: Serine/threonine-protein kinase PAK 4
O: Serine/threonine-protein kinase PAK 4
P: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,56643
Polymers192,73216
Non-polymers4,83427
Water20,3931132
1
A: Ras-related C3 botulinum toxin substrate 3
I: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7086
Polymers24,0912
Non-polymers6164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-47 kcal/mol
Surface area10040 Å2
MethodPISA
2
B: Ras-related C3 botulinum toxin substrate 3
J: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6725
Polymers24,0912
Non-polymers5813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-46 kcal/mol
Surface area10250 Å2
MethodPISA
3
C: Ras-related C3 botulinum toxin substrate 3
K: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7346
Polymers24,0912
Non-polymers6434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-27 kcal/mol
Surface area10020 Å2
MethodPISA
4
D: Ras-related C3 botulinum toxin substrate 3
L: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6995
Polymers24,0912
Non-polymers6083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-27 kcal/mol
Surface area10270 Å2
MethodPISA
5
E: Ras-related C3 botulinum toxin substrate 3
M: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6725
Polymers24,0912
Non-polymers5813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-37 kcal/mol
Surface area10030 Å2
MethodPISA
6
F: Ras-related C3 botulinum toxin substrate 3
N: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7346
Polymers24,0912
Non-polymers6434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-35 kcal/mol
Surface area10050 Å2
MethodPISA
7
G: Ras-related C3 botulinum toxin substrate 3
O: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6725
Polymers24,0912
Non-polymers5813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-36 kcal/mol
Surface area10020 Å2
MethodPISA
8
H: Ras-related C3 botulinum toxin substrate 3
P: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6725
Polymers24,0912
Non-polymers5813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-36 kcal/mol
Surface area10170 Å2
MethodPISA
9
E: Ras-related C3 botulinum toxin substrate 3
H: Ras-related C3 botulinum toxin substrate 3
M: Serine/threonine-protein kinase PAK 4
P: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34510
Polymers48,1834
Non-polymers1,1626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-85 kcal/mol
Surface area18430 Å2
MethodPISA
10
A: Ras-related C3 botulinum toxin substrate 3
B: Ras-related C3 botulinum toxin substrate 3
I: Serine/threonine-protein kinase PAK 4
J: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,38011
Polymers48,1834
Non-polymers1,1977
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-103 kcal/mol
Surface area18580 Å2
MethodPISA
11
C: Ras-related C3 botulinum toxin substrate 3
K: Serine/threonine-protein kinase PAK 4
hetero molecules

D: Ras-related C3 botulinum toxin substrate 3
L: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,43411
Polymers48,1834
Non-polymers1,2517
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area8350 Å2
ΔGint-61 kcal/mol
Surface area18540 Å2
MethodPISA
12
F: Ras-related C3 botulinum toxin substrate 3
N: Serine/threonine-protein kinase PAK 4
hetero molecules

G: Ras-related C3 botulinum toxin substrate 3
O: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,40711
Polymers48,1834
Non-polymers1,2247
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area8670 Å2
ΔGint-82 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.843, 73.859, 133.840
Angle α, β, γ (deg.)88.58, 87.76, 70.64
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12I
22J
32K
42L
52M
62N
72O
82P

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 1782 - 179
21METMETLEULEUBC1 - 1772 - 178
31METMETGLYGLYCD1 - 1782 - 179
41METMETGLYGLYDF1 - 1782 - 179
51GLNGLNGLYGLYEG2 - 1783 - 179
61METMETGLYGLYFB1 - 1782 - 179
71METMETGLYGLYGE1 - 1782 - 179
81METMETGLYGLYHH1 - 1782 - 179
12GLUGLUILEILEII10 - 431 - 34
22GLUGLUILEILEJJ10 - 431 - 34
32GLUGLUILEILEKK10 - 431 - 34
42GLUGLUILEILELL10 - 431 - 34
52GLUGLUILEILEMM10 - 431 - 34
62GLUGLUILEILENN10 - 431 - 34
72GLUGLUILEILEOO10 - 431 - 34
82GLUGLULEULEUPP10 - 421 - 33

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 16 molecules AFBCGDEHIJKLMNOP

#1: Protein
Ras-related C3 botulinum toxin substrate 3 / RAC3 / p21-Rac3


Mass: 19934.928 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P60763
#2: Protein/peptide
Serine/threonine-protein kinase PAK 4 / PAK4 / p21-activated kinase 4 / PAK-4


Mass: 4156.529 Da / Num. of mol.: 8 / Fragment: CRIB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: O96013, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 1159 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Citrate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9687 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.1→62.11 Å / Num. obs: 106111 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.9 / Num. unique all: 44621 / Rsym value: 0.602 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G0N

2g0n


Resolution: 2.1→62.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.181 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22453 5292 5 %RANDOM
Rwork0.1719 ---
all0.1745 100750 --
obs0.1745 100750 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.184 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å2-0.42 Å2-0.04 Å2
2---0.09 Å20.02 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12994 0 284 1132 14410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213676
X-RAY DIFFRACTIONr_bond_other_d0.0010.028891
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.98418750
X-RAY DIFFRACTIONr_angle_other_deg0.968321762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09351718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70923.641541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.691152048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0161568
X-RAY DIFFRACTIONr_chiral_restr0.0860.22143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022749
X-RAY DIFFRACTIONr_nbd_refined0.2010.22549
X-RAY DIFFRACTIONr_nbd_other0.1930.29118
X-RAY DIFFRACTIONr_nbtor_refined0.1780.26529
X-RAY DIFFRACTIONr_nbtor_other0.0860.26667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2859
X-RAY DIFFRACTIONr_metal_ion_refined0.060.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.242
X-RAY DIFFRACTIONr_mcbond_it0.4861.58826
X-RAY DIFFRACTIONr_mcbond_other0.141.53410
X-RAY DIFFRACTIONr_mcangle_it0.799213817
X-RAY DIFFRACTIONr_scbond_it1.42335729
X-RAY DIFFRACTIONr_scangle_it2.1384.54915
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1019medium positional0.190.5
12B1019medium positional0.240.5
13C1019medium positional0.190.5
14D1019medium positional0.190.5
15E1019medium positional0.160.5
16F1019medium positional0.170.5
17G1019medium positional0.170.5
18H1019medium positional0.190.5
21I191medium positional0.160.5
22J191medium positional0.180.5
23K191medium positional0.210.5
24L191medium positional0.170.5
25M191medium positional0.150.5
26N191medium positional0.190.5
27O191medium positional0.190.5
28P191medium positional0.180.5
11A1112loose positional0.55
12B1112loose positional0.375
13C1112loose positional0.525
14D1112loose positional0.385
15E1112loose positional0.355
16F1112loose positional0.335
17G1112loose positional0.455
18H1112loose positional0.385
21I203loose positional0.455
22J203loose positional0.335
23K203loose positional0.515
24L203loose positional0.655
25M203loose positional0.55
26N203loose positional0.445
27O203loose positional0.385
28P203loose positional0.475
11A1019medium thermal0.532
12B1019medium thermal0.622
13C1019medium thermal0.542
14D1019medium thermal0.462
15E1019medium thermal0.472
16F1019medium thermal0.492
17G1019medium thermal0.472
18H1019medium thermal0.542
21I191medium thermal0.612
22J191medium thermal0.532
23K191medium thermal0.562
24L191medium thermal0.532
25M191medium thermal0.412
26N191medium thermal0.552
27O191medium thermal0.432
28P191medium thermal0.432
11A1112loose thermal1.1610
12B1112loose thermal1.2410
13C1112loose thermal1.0910
14D1112loose thermal1.3210
15E1112loose thermal1.1210
16F1112loose thermal1.2710
17G1112loose thermal1.1110
18H1112loose thermal1.1310
21I203loose thermal0.9710
22J203loose thermal1.110
23K203loose thermal1.5810
24L203loose thermal1.2110
25M203loose thermal1.1210
26N203loose thermal0.8610
27O203loose thermal1.1710
28P203loose thermal110
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 386 -
Rwork0.239 6491 -
obs--86.87 %
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)
11.34250.0952-0.44531.1562-0.19271.6311-0.0251-0.10740.06210.0206-0.0054-0.0601-0.1070.07060.0304-0.21910.0408-0.0205-0.1562-0.0147-0.1359-14.1773-25.346522.6672
21.4878-0.47580.15970.696-0.10751.43990.05230.144-0.1059-0.0868-0.05670.0520.12890.04870.0044-0.19710.02980.0113-0.1264-0.0178-0.1193.8172-47.19989.5628
31.2809-0.11860.18691.4064-0.72692.44420.00710.1191-0.00680.049-0.0651-0.0024-0.12780.14750.058-0.20680.01910.0045-0.1433-0.0094-0.147515.978-54.030245.2454
40.69380.104-0.08512.41270.50022.33780.058-0.0785-0.13390.3717-0.0361-0.16430.2670.087-0.0219-0.07280.0589-0.0173-0.13990.0212-0.1151-9.1043-12.463858.2962
50.64850.22020.12931.70490.18751.2967-0.0246-0.0412-0.0546-0.0870.0897-0.0793-0.08390.1031-0.0651-0.15690.00010.0094-0.12520.0002-0.1553-15.8781-17.2739-9.7406
61.05930.15350.14631.3051-0.48881.6383-0.0804-0.01720.0443-0.00960.08960.08640.0065-0.1359-0.0092-0.1003-0.02790.0054-0.16390.0077-0.1504-0.4837-61.9647-28.8754
70.9051-0.2841-0.15190.7371-0.13572.08530.0667-0.0112-0.0264-0.0451-0.0524-0.0262-0.030.055-0.0144-0.0607-0.0267-0.0156-0.19590.007-0.153912.0359-46.609377.3963
81.6358-0.8151-0.57321.41780.46811.84210.2053-0.11160.1184-0.2317-0.0009-0.114-0.28780.1097-0.2044-0.0054-0.07280.056-0.1747-0.0157-0.1418-1.4564-22.851-36.7939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1782 - 179
2X-RAY DIFFRACTION1II10 - 431 - 34
3X-RAY DIFFRACTION2BC1 - 1772 - 178
4X-RAY DIFFRACTION2JJ11 - 442 - 35
5X-RAY DIFFRACTION3CD1 - 1782 - 179
6X-RAY DIFFRACTION3KK10 - 431 - 34
7X-RAY DIFFRACTION4DF1 - 1782 - 179
8X-RAY DIFFRACTION4LL10 - 441 - 35
9X-RAY DIFFRACTION5EG2 - 1783 - 179
10X-RAY DIFFRACTION5MM10 - 431 - 34
11X-RAY DIFFRACTION6FB1 - 1782 - 179
12X-RAY DIFFRACTION6NN10 - 441 - 35
13X-RAY DIFFRACTION7GE1 - 1782 - 179
14X-RAY DIFFRACTION7OO10 - 431 - 34
15X-RAY DIFFRACTION8HH1 - 1782 - 179
16X-RAY DIFFRACTION8PP10 - 421 - 33

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