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- PDB-3cxl: Crystal structure of human chimerin 1 (CHN1) -

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Basic information

Entry
Database: PDB / ID: 3cxl
TitleCrystal structure of human chimerin 1 (CHN1)
ComponentsN-chimerin
KeywordsSIGNALING PROTEIN / SH2 / RHO-GAP / C1 / Structural Genomics Consortium / SGC / GTPase activation / Metal-binding / Phorbol-ester binding / SH2 domain / Zinc-finger
Function / homology
Function and homology information


motor neuron axon guidance / regulation of small GTPase mediated signal transduction / regulation of axonogenesis / CDC42 GTPase cycle / ephrin receptor signaling pathway / RAC1 GTPase cycle / GTPase activator activity / ephrin receptor binding / metal ion binding / cytosol
Similarity search - Function
Chimaerin / Chimaerin, SH2 domain / Chimaerin, RhoGAP domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...Chimaerin / Chimaerin, SH2 domain / Chimaerin, RhoGAP domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsShen, L. / Buck, M. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. ...Shen, L. / Buck, M. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human chimerin 1 (CHN1).
Authors: Shen, L. / Buck, M. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Derived calculations
Category: phasing / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_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 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: N-chimerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9294
Polymers53,7991
Non-polymers1313
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.187, 152.187, 69.529
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein N-chimerin / NC / N-chimaerin / Alpha-chimerin / A-chimaerin / Rho GTPase-activating protein 2


Mass: 53798.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHN1, ARHGAP2, CHN / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P15882
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsRESIDUES A161-A167 THAT ARE PRESENT IN COORDINATES ARE LIKELY PART OF ENTITY 1. THEY WERE MODELED ...RESIDUES A161-A167 THAT ARE PRESENT IN COORDINATES ARE LIKELY PART OF ENTITY 1. THEY WERE MODELED AS POLY-ALA. THEIR ASSIGNMENT TO THE AMINO ACID SEQUENCE OF THE PROTEIN IS UNKNOWN DUE TO LACK OF CONTINUOUS ELECTRON DENSITY.

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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: 4.32 Å3/Da / Density % sol: 71.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.4M Ammonium sulfate, 0.1M Glycine, 0.01M Magnesium chloride, 5% MPD, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29085 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.082 / Χ2: 1.994 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.649.20.9713591.417197.3
2.64-2.699.80.86814691.521199.9
2.69-2.7410.50.77414381.3621100
2.74-2.8110.68114471.4041100
2.8-2.8611.20.53914611.3211100
2.86-2.9311.20.4514491.4051100
2.93-311.20.35114571.3561100
3-3.0811.20.26814401.4521100
3.08-3.1711.30.21814571.4271100
3.17-3.2811.20.16814291.5311100
3.28-3.3911.20.11714641.6661100
3.39-3.5311.20.09814661.8381100
3.53-3.6911.20.07714581.8571100
3.69-3.8811.10.06714412.1361100
3.88-4.13110.06114742.4641100
4.13-4.4510.90.05614642.9241100
4.45-4.8910.60.05714593.5231100
4.89-5.610.40.05714743.5831100
5.6-7.0510.20.05114963.0011100
7.05-50100.03814832.805197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.57 Å43.93 Å
Translation2.57 Å43.93 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1XA6, 2OSA

1xa6

2osa


Resolution: 2.6→28.513 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.298 / WRfactor Rwork: 0.263 / SU B: 25.513 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Atomic B-factors are residuals from TLS refinement. 3. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement. 4. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Atomic B-factors are residuals from TLS refinement. 3. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement. 4. Residues A 161 through A 167 are likely part of entity 1. They were modeled as poly-Ala due to insufficient electron density. Their assignment to the amino acid sequence is unknown due to lack of continuous electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1433 5.062 %RANDOM
Rwork0.266 ---
obs0.267 28308 99.546 %-
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: 48.663 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20.022 Å20 Å2
2--0.044 Å20 Å2
3----0.067 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 3 0 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223245
X-RAY DIFFRACTIONr_bond_other_d0.0020.022184
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9634392
X-RAY DIFFRACTIONr_angle_other_deg0.8153.0025306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2115399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7923.537147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0315547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0591521
X-RAY DIFFRACTIONr_chiral_restr0.0570.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
X-RAY DIFFRACTIONr_nbd_refined0.2180.2709
X-RAY DIFFRACTIONr_nbd_other0.1730.22152
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21577
X-RAY DIFFRACTIONr_nbtor_other0.0820.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0630.21
X-RAY DIFFRACTIONr_mcbond_it0.3421.52066
X-RAY DIFFRACTIONr_mcbond_other0.0521.5806
X-RAY DIFFRACTIONr_mcangle_it0.57623215
X-RAY DIFFRACTIONr_scbond_it0.79231346
X-RAY DIFFRACTIONr_scangle_it1.2414.51177
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 (%)
2.6-2.6670.444990.4211968209598.663
2.667-2.740.4431020.3661863198499.042
2.74-2.8190.363960.3311868197899.292
2.819-2.9040.336860.31823191899.531
2.904-2.9990.316910.2861758185399.784
2.999-3.1030.291890.2611693178999.609
3.103-3.2180.321870.2761645173799.712
3.218-3.3480.285890.2661572166399.88
3.348-3.4950.29710.25315521623100
3.495-3.6620.282820.2511432151599.934
3.662-3.8570.307750.26613891464100
3.857-4.0860.319710.2631328140199.857
4.086-4.3620.326630.2461241130599.923
4.362-4.7020.269650.2381150121899.754
4.702-5.1370.212590.23510631122100
5.137-5.720.272600.2519751035100
5.72-6.5620.369550.295849904100
6.562-7.9320.295430.27762805100
7.932-10.8070.266310.23458462099.194
10.807-28.5130.277190.28836040892.892
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)
15.10531.0507-1.96721.0828-0.68161.6257-0.0362-0.2221-0.1670.1175-0.1364-0.11850.06470.2060.1726-0.05720.01510.036-0.098-0.0171-0.1771-2.313267.0689-0.0287
24.31190.9578-0.00273.0188-1.0793.515-0.16840.4739-0.5878-0.48590.0966-0.07270.3836-0.0660.07180.0295-0.0490.1072-0.0767-0.18380.0276-30.197548.8915-8.4562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 26218 - 266
2X-RAY DIFFRACTION2AA263 - 455267 - 459

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