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- PDB-2p67: Crystal structure of LAO/AO transport system kinase -

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Basic information

Entry
Database: PDB / ID: 2p67
TitleCrystal structure of LAO/AO transport system kinase
ComponentsLAO/AO transport system kinase
KeywordsTRANSFERASE / argK / Kinase / LAO/AO transport system kinase / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP binding / cytoplasm
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsRamagopal, U.A. / Adams, J. / Rodgers, L. / Toro, R. / Bain, K. / Rutter, M. / Schwinn, K. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of LAO/AO transport system kinase
Authors: Ramagopal, U.A. / Adams, J. / Rodgers, L. / Toro, R. / Bain, K. / Rutter, M. / Schwinn, K. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAO/AO transport system kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1296
Polymers37,9641
Non-polymers1655
Water3,819212
1
A: LAO/AO transport system kinase
hetero molecules

A: LAO/AO transport system kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25812
Polymers75,9282
Non-polymers33010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6440 Å2
ΔGint-87 kcal/mol
Surface area28120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.311, 108.452, 141.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsBiological unit is a domain swapped dimer

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Components

#1: Protein LAO/AO transport system kinase


Mass: 37964.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: argK, b2918, JW2885 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P27254, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.5 M NaCl, 10% MPD, 0.1M CAPS pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X3A10.9793
SYNCHROTRONNSLS X29A20.9793
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDFeb 27, 2007
ADSC QUANTUM 3152CCDFeb 27, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21
ReflectionResolution: 1.8→50 Å / Num. all: 40015 / Num. obs: 40015 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.051 / Rsym value: 0.041 / Χ2: 0.673 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3999 / Rsym value: 0.424 / Χ2: 0.283 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→43.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.457 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2006 5 %RANDOM
Rwork0.207 ---
all0.208 39802 --
obs0.208 39802 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 5 212 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222497
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9663394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8345326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63823.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82315462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021876
X-RAY DIFFRACTIONr_nbd_refined0.2080.21119
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.222
X-RAY DIFFRACTIONr_mcbond_it0.8141.51543
X-RAY DIFFRACTIONr_mcangle_it1.52322498
X-RAY DIFFRACTIONr_scbond_it2.3013975
X-RAY DIFFRACTIONr_scangle_it3.9144.5884
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 144 -
Rwork0.277 2695 -
obs-2839 96.96 %

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