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- PDB-4fh0: Crystal Structure of Human BinCARD CARD, double mutant F16M/L66M ... -

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Basic information

Entry
Database: PDB / ID: 4fh0
TitleCrystal Structure of Human BinCARD CARD, double mutant F16M/L66M SeMet form
ComponentsBcl10-interacting CARD protein
KeywordsIMMUNE SYSTEM / Apoptosis / Mainly alpha / Bcl10 / Nucleus / ER / Mitochondria
Function / homology
Function and homology information


CARD domain binding / negative regulation of canonical NF-kappaB signal transduction / mitochondrial membrane / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
BinCARD, CARD domain / Caspase recruitment domain-containing protein 19 / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Caspase recruitment domain-containing protein 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsChen, K.-E. / Kobe, B. / Martin, J.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of the caspase recruitment domain of BinCARD reveals that all three cysteines can be oxidized.
Authors: Chen, K.E. / Richards, A.A. / Caradoc-Davies, T.T. / Vajjhala, P.R. / Robin, G. / Lua, L.H. / Hill, J.M. / Schroder, K. / Sweet, M.J. / Kellie, S. / Kobe, B. / Martin, J.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / refln / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl10-interacting CARD protein
B: Bcl10-interacting CARD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5595
Polymers24,2712
Non-polymers2883
Water3,639202
1
A: Bcl10-interacting CARD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3283
Polymers12,1351
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bcl10-interacting CARD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2322
Polymers12,1351
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.196, 36.669, 43.276
Angle α, β, γ (deg.)108.54, 90.30, 111.01
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a monomer. There is 2 biological unit in the asymmetric unit

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Components

#1: Protein Bcl10-interacting CARD protein / BinCARD


Mass: 12135.491 Da / Num. of mol.: 2 / Fragment: caspase recruitment domain / Mutation: F16M, L66M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf89 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96LW7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.94 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: Bis-Tris pH 6.5, ammonium sulfate, PEG 3350, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537, 0.9797, 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2009
RadiationMonochromator: Sagitally focused Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97971
30.97951
ReflectionResolution: 1.25→32.139 Å / Num. all: 45786 / Num. obs: 45785 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 12 Å2 / Limit h max: 25 / Limit h min: -25 / Limit k max: 27 / Limit k min: -29 / Limit l max: 34 / Limit l min: 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection scaleGroup code: 1
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6572 / % possible all: 92.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHARPphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
Blu-IceGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.4→27.724 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9167 / SU ML: 0.27 / σ(F): 2.44 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 1676 5.08 %Random
Rwork0.1374 ---
obs0.1395 32992 96.52 %-
all-32997 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.123 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 49.37 Å2 / Biso mean: 17.6784 Å2 / Biso min: 6.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.0894 Å2-0.0136 Å2-0.1957 Å2
2---0.3114 Å2-0.6843 Å2
3---0.222 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.4→27.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 15 202 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011686
X-RAY DIFFRACTIONf_angle_d1.3032282
X-RAY DIFFRACTIONf_chiral_restr0.076243
X-RAY DIFFRACTIONf_plane_restr0.007299
X-RAY DIFFRACTIONf_dihedral_angle_d13.934682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4001-1.44130.20341380.1422458259692
1.4413-1.48780.18131530.12352577273095
1.4878-1.5410.18271380.11532606274496
1.541-1.60270.17481270.11752603273096
1.6027-1.67560.1931270.12462626275396
1.6756-1.76390.19451360.12892608274497
1.7639-1.87440.19711450.1312623276897
1.8744-2.01910.18181400.12692631277198
2.0191-2.22220.14941370.12662630276798
2.2222-2.54360.16411400.132657279798
2.5436-3.20390.1791520.14742684283699
3.2039-27.72930.17661430.15552613275697

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