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- PDB-3ney: Crystal structure of the kinase domain of MPP1/p55 -

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Basic information

Entry
Database: PDB / ID: 3ney
TitleCrystal structure of the kinase domain of MPP1/p55
Components55 kDa erythrocyte membrane protein
KeywordsMEMBRANE PROTEIN / structural genomics consortium / sgc / 55 kDa erythrocyte membrane protein
Function / homology
Function and homology information


regulation of neutrophil chemotaxis / GMP kinase activity / stereocilium / Sensory processing of sound by outer hair cells of the cochlea / cortical cytoskeleton / centriolar satellite / cell-cell junction / signaling receptor binding / signal transduction / membrane / plasma membrane
Similarity search - Function
MPP1, SH3 domain / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase ...MPP1, SH3 domain / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
55 kDa erythrocyte membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsShen, Y. / Tong, Y. / Zhong, N. / Guan, X. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Shen, Y. / Tong, Y. / Zhong, N. / Guan, X. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the kinase domain of MPP1/p55
Authors: Shen, Y. / Tong, Y. / Zhong, N. / Guan, X. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Data collection
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 55 kDa erythrocyte membrane protein
B: 55 kDa erythrocyte membrane protein
C: 55 kDa erythrocyte membrane protein
D: 55 kDa erythrocyte membrane protein
F: 55 kDa erythrocyte membrane protein
E: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,51449
Polymers135,3626
Non-polymers1,15343
Water3,621201
1
A: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,75210
Polymers22,5601
Non-polymers1929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,94511
Polymers22,5601
Non-polymers38410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7528
Polymers22,5601
Non-polymers1927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7528
Polymers22,5601
Non-polymers1927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6566
Polymers22,5601
Non-polymers965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: 55 kDa erythrocyte membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6566
Polymers22,5601
Non-polymers965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.088, 131.562, 237.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
55 kDa erythrocyte membrane protein / p55 / Membrane protein / palmitoylated 1


Mass: 22560.275 Da / Num. of mol.: 6 / Fragment: Kinase domain, residues 282-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP1, DXS552E, EMP55 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q00013
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.15 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.6M ammonium sulfate, 0.01M magnesium chloride, 0.1M sodium cacodylate. The sample solution also contained 0.002M GDP, 0.002M ADP, 0.005M magnesium chloride. Crystal growth was incubated ...Details: 1.6M ammonium sulfate, 0.01M magnesium chloride, 0.1M sodium cacodylate. The sample solution also contained 0.002M GDP, 0.002M ADP, 0.005M magnesium chloride. Crystal growth was incubated for 5 months., pH 5.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 106079 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.165 / Χ2: 1.672 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.334.90.963103301.259198.7
2.33-2.425.70.931104451.271199.9
2.42-2.536.10.765104921.2851100
2.53-2.676.30.625105561.3571100
2.67-2.836.30.441105151.4331100
2.83-3.056.30.279105731.6481100
3.05-3.366.30.164106141.7021100
3.36-3.856.20.099106501.8881100
3.85-4.846.10.076107802.5961100
4.84-4060.057111242.1061100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KGD

1kgd


Resolution: 2.26→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.214 / SU B: 5.899 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. PHENIX, COOT and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2121 2.009 %RANDOM
Rwork0.235 ---
obs0.236 105554 99.254 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.726 Å2
Baniso -1Baniso -2Baniso -3
1--2.158 Å20 Å20 Å2
2--0.399 Å20 Å2
3---1.759 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8355 0 91 201 8647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228662
X-RAY DIFFRACTIONr_bond_other_d0.0010.025736
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.95311779
X-RAY DIFFRACTIONr_angle_other_deg0.866314046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03251091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17224.795415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.167151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961541
X-RAY DIFFRACTIONr_chiral_restr0.0840.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021725
X-RAY DIFFRACTIONr_mcbond_it0.8941.55398
X-RAY DIFFRACTIONr_mcbond_other0.1671.52162
X-RAY DIFFRACTIONr_mcangle_it1.74628735
X-RAY DIFFRACTIONr_scbond_it2.58133264
X-RAY DIFFRACTIONr_scangle_it4.3544.53032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.31800.3217295775594.068
2.318-2.3810.3661920.317288751599.534
2.381-2.450.3271780.2847101729799.753
2.45-2.5250.3261730.2676958714599.804
2.525-2.6070.2951610.2576774694699.842
2.607-2.6980.293530.2526615668899.701
2.698-2.7990.292940.2476365647699.737
2.799-2.9120.261310.2326102625599.648
2.912-3.040.2621450.2275836600399.634
3.04-3.1870.2931230.2335597573999.669
3.187-3.3570.2671980.2325257547999.562
3.357-3.5580.254980.2165100521699.655
3.558-3.80.246900.2114796490399.653
3.8-4.0990.223770.24466455599.737
4.099-4.4820.2241380.1884100425399.647
4.482-4.9970.179500.1823786385099.636
4.997-5.7440.27710.2353358345199.363
5.744-6.9710.33730.2922875296099.595
6.971-9.6030.229470.2472301236399.365
9.603-300.456290.2671463149899.599

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