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- PDB-2oai: The structure of transporter associated domain CorC_HlyC from a X... -

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Basic information

Entry
Database: PDB / ID: 2oai
TitleThe structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin.
ComponentsHemolysin
KeywordsTOXIN / pfam03471 / Xylella fastidiosa Temecula1 / hemolysin / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Volkart, L. / Abdullah, J. / Binkowski, T.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin.
Authors: Cuff, M.E. / Volkart, L. / Abdullah, J. / Binkowski, T.A. / Joachimiak, A.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT SINCE THIS IS A PROTEIN FRAGMENT, THE BIOLOGICAL UNIT IS UNKNOWN. THE DIMERIC ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9595
Polymers10,7551
Non-polymers2044
Water1,54986
1
A: Hemolysin
hetero molecules

A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,91810
Polymers21,5092
Non-polymers4098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2940 Å2
ΔGint-48 kcal/mol
Surface area8130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.905, 87.905, 87.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsBiological assembly is most likely a dimer, the second generated by about a 2-fold: x,1-y,-z

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Components

#1: Protein Hemolysin


Mass: 10754.613 Da / Num. of mol.: 1 / Fragment: CorC_HlyC Domain: Residues 349-439
Source method: isolated from a genetically manipulated source
Details: Authors state that although this protein is a fragment of a putative hemolysin (a toxin), the function of this domain is unknown
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Temecula1 / Gene: tlyC / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87DZ3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M CaCl2, 0.1M Bis-Tris pH 6.5, 30% PEG MME550, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97938, 0.98706
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979381
30.987061
ReflectionResolution: 1.8→31.1 Å / Num. all: 10567 / Num. obs: 10567 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.043 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.549 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.8→31.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.906 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19977 503 4.8 %RANDOM
Rwork0.1746 ---
all0.17583 10064 --
obs0.17583 10064 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.966 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms644 0 10 86 740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021682
X-RAY DIFFRACTIONr_angle_refined_deg1.631.974922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.903583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33323.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28415112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.772157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02520
X-RAY DIFFRACTIONr_nbd_refined0.2150.2341
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.264
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1730.24
X-RAY DIFFRACTIONr_mcbond_it1.6381.5412
X-RAY DIFFRACTIONr_mcangle_it1.8082646
X-RAY DIFFRACTIONr_scbond_it2.643306
X-RAY DIFFRACTIONr_scangle_it4.0174.5275
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 35 -
Rwork0.252 686 -
obs--92.08 %
Refinement TLS params.Method: refined / Origin x: 20.7384 Å / Origin y: 33.6651 Å / Origin z: 2.6582 Å
111213212223313233
T-0.3127 Å20.0008 Å20.0308 Å2--0.2861 Å20.053 Å2---0.2491 Å2
L2.8206 °2-1.0535 °2-0.4461 °2-3.8898 °2-0.2992 °2--3.1894 °2
S0.0753 Å °0.0155 Å °-0.3113 Å °0.081 Å °-0.3677 Å °-0.1354 Å °0.446 Å °0.0355 Å °0.2924 Å °

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