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- PDB-4m9q: Crystal structure of C-terminally truncated Arl13B from Chlamydom... -

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Basic information

Entry
Database: PDB / ID: 4m9q
TitleCrystal structure of C-terminally truncated Arl13B from Chlamydomonas rheinhardtii bound to GppNHp
ComponentsARF-like GTPase
KeywordsHYDROLASE / GTPase / G domain / Joubert Syndrome / cilia
Function / homology
Function and homology information


ciliary membrane / GTPase activity / GTP binding
Similarity search - Function
: / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...: / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor-like protein 13B
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiertzschke, M. / Koerner, C. / Spoerner, M. / Wittinghofer, A.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural insights into the small G-protein Arl13B and implications for Joubert syndrome.
Authors: Miertzschke, M. / Koerner, C. / Spoerner, M. / Wittinghofer, A.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Apr 9, 2014Group: Experimental preparation
Revision 1.4Sep 20, 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_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_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: ARF-like GTPase
B: ARF-like GTPase
C: ARF-like GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,48512
Polymers77,5573
Non-polymers1,9289
Water1,17165
1
A: ARF-like GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4954
Polymers25,8521
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARF-like GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4954
Polymers25,8521
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ARF-like GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4954
Polymers25,8521
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.050, 76.830, 172.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A18 - 211
2112B18 - 211
3112C18 - 211

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.441507, 0.896486, -0.037214), (-0.896638, 0.442364, 0.018845), (0.033357, 0.025047, 0.99913)4.28349, 12.75831, 28.20193
3given(0.447433, -0.891721, -0.068101), (0.894093, 0.447729, 0.011701), (0.020056, -0.066124, 0.99761)5.60781, -10.11759, -28.93787

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Components

#1: Protein ARF-like GTPase / Arl13B


Mass: 25852.311 Da / Num. of mol.: 3 / Fragment: UNP residues 18-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ARL13, CHLREDRAFT_195529 / Production host: Escherichia coli (E. coli) / References: UniProt: A8INQ0, small monomeric GTPase
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 30% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2012
RadiationMonochromator: silicon mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→19.83 Å / Num. all: 22958 / Num. obs: 22891 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rsym value: 0.065 / Net I/σ(I): 30.03
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 5.78 / Rsym value: 0.519 / % possible all: 100

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KSH

1ksh


Resolution: 2.5→19.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.783 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.746 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23536 1145 5 %RANDOM
Rwork0.18969 ---
obs0.192 21746 99.71 %-
all-22891 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.618 Å2
Baniso -1Baniso -2Baniso -3
1-6.03 Å20 Å20 Å2
2---2.89 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 114 65 4687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194958
X-RAY DIFFRACTIONr_bond_other_d0.0020.023393
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9896756
X-RAY DIFFRACTIONr_angle_other_deg1.01738278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11824.097227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.47215867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21542
X-RAY DIFFRACTIONr_chiral_restr0.0990.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215590
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021008
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1146MEDIUM POSITIONAL0.040.5
2B1146MEDIUM POSITIONAL0.050.5
3C1146MEDIUM POSITIONAL0.050.5
1A977TIGHT THERMAL3.870.5
2B977TIGHT THERMAL4.790.5
3C977TIGHT THERMAL4.020.5
1A1146MEDIUM THERMAL4.222
2B1146MEDIUM THERMAL5.142
3C1146MEDIUM THERMAL4.252
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 76 -
Rwork0.28 1410 -
obs--100 %
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)
12.18290.0845-0.49696.4537-0.50983.1690.0958-0.04580.0643-0.0948-0.2476-0.2509-0.08790.34620.15180.0927-0.00310.05670.04720.03420.074111.9325-5.3397-41.5916
24.9834-1.7672-0.74024.55650.28566.0804-0.12650.20080.15980.3242-0.01810.0555-0.6135-0.23590.14460.1280.0213-0.00740.04710.03090.040417.4686-2.7077-70.5041
33.56831.6012-0.19114.78271.68856.5329-0.02-0.18330.1434-0.0088-0.40160.17710.4603-0.28590.42160.0774-0.04910.06580.0973-0.04370.07766.399-2.3734-12.5184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 211
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B18 - 213
4X-RAY DIFFRACTION2B301 - 302
5X-RAY DIFFRACTION3C16 - 208
6X-RAY DIFFRACTION3C301 - 302

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