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- PDB-6cpy: Structure of apo GRMZM2G135359 pseudokinase -

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Basic information

Entry
Database: PDB / ID: 6cpy
TitleStructure of apo GRMZM2G135359 pseudokinase
ComponentsGRMZM2G135359 pseudokinase
KeywordsTRANSFERASE / Receptor-like kinase / pseudokinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein kinase activity / protein phosphorylation / ATP binding / membrane
Similarity search - Function
Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein kinase domain-containing protein / Protein kinase superfamily protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAquino, B. / Counago, R.M. / Godoi, P.H.C. / Massirer, K.B. / Elkins, J.M. / Arruda, P. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To be Published
Title: Structure of apo GRMZM2G135359 pseudokinase
Authors: Aquino, B. / Counago, R.M. / Godoi, P.H.C. / Massirer, K.B. / Elkins, J.M. / Arruda, P.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRMZM2G135359 pseudokinase
B: GRMZM2G135359 pseudokinase


Theoretical massNumber of molelcules
Total (without water)69,5712
Polymers69,5712
Non-polymers00
Water3,531196
1
A: GRMZM2G135359 pseudokinase


Theoretical massNumber of molelcules
Total (without water)34,7861
Polymers34,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRMZM2G135359 pseudokinase


Theoretical massNumber of molelcules
Total (without water)34,7861
Polymers34,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.492, 61.496, 144.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GRMZM2G135359 pseudokinase


Mass: 34785.602 Da / Num. of mol.: 2 / Fragment: UNP residues 183-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4F901, UniProt: C0P4K9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.15 M potassium bromide, 30% PEG2000 MME / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER 16M / Detector: PIXEL / Date: Jun 28, 2017
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→19.82 Å / Num. obs: 61213 / % possible obs: 99.9 % / Redundancy: 10.88 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 2.035 / CC1/2: 0.519 / Rpim(I) all: 0.943 / Rrim(I) all: 2.247 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UV4

5uv4


Resolution: 1.7→19.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.756 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21529 2974 4.9 %RANDOM
Rwork0.1994 ---
obs0.20021 58167 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.262 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å2-0 Å2
2---1.32 Å20 Å2
3---2.55 Å2
Refinement stepCycle: 1 / Resolution: 1.7→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 196 4400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194321
X-RAY DIFFRACTIONr_bond_other_d0.0010.023998
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9615842
X-RAY DIFFRACTIONr_angle_other_deg0.73739255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94823.387186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.951532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6713.3752164
X-RAY DIFFRACTIONr_mcbond_other1.6643.3752163
X-RAY DIFFRACTIONr_mcangle_it2.675.0452699
X-RAY DIFFRACTIONr_mcangle_other2.6715.0452700
X-RAY DIFFRACTIONr_scbond_it2.0373.6082157
X-RAY DIFFRACTIONr_scbond_other2.0373.6082158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2995.3283142
X-RAY DIFFRACTIONr_long_range_B_refined4.64539.6754810
X-RAY DIFFRACTIONr_long_range_B_other4.62639.5774791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 229 -
Rwork0.312 4245 -
obs--99.82 %

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