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- PDB-2irm: Crystal structure of mitogen-activated protein kinase kinase kina... -

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Basic information

Entry
Database: PDB / ID: 2irm
TitleCrystal structure of mitogen-activated protein kinase kinase kinase 7 interacting protein 1 from Anopheles gambiae
Componentsmitogen-activated protein kinase kinase kinase 7 interacting protein 1
KeywordsTRANSFERASE / TAK1-binding protein / TAB1 / mitogen-activated protein kinase kinase kinase 7 interacting protein 1 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity
Similarity search - Function
PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJin, X. / Bonanno, J.B. / Pelletier, L. / Freeman, J.C. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Shapiro, L. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionOct 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Aug 30, 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
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: mitogen-activated protein kinase kinase kinase 7 interacting protein 1


Theoretical massNumber of molelcules
Total (without water)39,6971
Polymers39,6971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.773, 73.773, 74.509
Angle α, β, γ (deg.)90.00, 116.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein mitogen-activated protein kinase kinase kinase 7 interacting protein 1


Mass: 39696.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Plasmid: BS-pSGX4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / References: UniProt: Q7QD46

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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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.2M Lithium Sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 27302 / Num. obs: 14971 / % possible obs: 55 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.047 / Rsym value: 0.037 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1919 / Rsym value: 0.189 / % possible all: 60

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2j4o, modified

2j4o


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 40.14 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 3.732 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27736 550 5 %RANDOM
Rwork0.21821 ---
obs0.22117 10523 93.25 %-
all-27302 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.178 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-3.68 Å2
2--4.16 Å20 Å2
3----6.02 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 0 0 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212648
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9523587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85524.841126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.75615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021995
X-RAY DIFFRACTIONr_nbd_refined0.2290.21231
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.21
X-RAY DIFFRACTIONr_mcbond_it0.3411.51714
X-RAY DIFFRACTIONr_mcangle_it0.61822690
X-RAY DIFFRACTIONr_scbond_it0.7531017
X-RAY DIFFRACTIONr_scangle_it1.2844.5897
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 25 -
Rwork0.279 629 -
obs--75.87 %
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)
12.8740.2531.15335.00552.80545.6472-0.0349-0.47830.22250.5312-0.3004-0.1107-0.52180.02620.3353-0.0349-0.0805-0.04360.1339-0.005-0.12824.618-2.88922.732
23.34070.90650.66775.44942.6235.31920.0885-0.43630.4647-0.4242-0.85951.1955-0.6036-1.09060.7711-0.00950.0917-0.09950.3383-0.13830.0155-7.241-1.7418.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 2134 - 204
2X-RAY DIFFRACTION2AA214 - 357205 - 348

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