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- PDB-2uu8: X-ray structure of Ni, Ca concanavalin A at Ultra-high resolution... -

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Basic information

Entry
Database: PDB / ID: 2uu8
TitleX-ray structure of Ni, Ca concanavalin A at Ultra-high resolution (0. 94A)
ComponentsCONCANAVALIN
KeywordsLECTIN / CALCIUM / MANGANESE / METAL-BINDING / NI
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Concanavalin-A
Similarity search - Component
Biological speciesCANAVALIA ENSIFORMIS (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsAhmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The Determination of Protonation States in Proteins.
Authors: Ahmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R.
History
DepositionMar 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Feb 5, 2014Group: Refinement description
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CONCANAVALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7213
Polymers25,6221
Non-polymers992
Water5,170287
1
A: CONCANAVALIN
hetero molecules

A: CONCANAVALIN
hetero molecules

A: CONCANAVALIN
hetero molecules

A: CONCANAVALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,88512
Polymers102,4904
Non-polymers3958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10120 Å2
ΔGint-126.2 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.867, 86.049, 61.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CONCANAVALIN / CON A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANAVALIA ENSIFORMIS (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MATURE CHAIN IS FORMED THROUGH A POSTTRANSLATIONAL MODIFICATION AFTER THE REMOVAL OF THE SIGNAL ...THE MATURE CHAIN IS FORMED THROUGH A POSTTRANSLATIONAL MODIFICATION AFTER THE REMOVAL OF THE SIGNAL SEQUENCE. THERE IS A CLEAVAGE AFTER ASN AT POSITIONS 148, 163, AND 281 IS FOLLOWED BY TRANSPOSITION AND LIGATION OF RESIDUES 164-281 AND 30-148.A NEW PEPTIDE BOND IS FORMED BETWEEN THE RESIDUES 164-281 AND 30-140.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.8 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.67
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2004
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67 Å / Relative weight: 1
ReflectionResolution: 0.94→33.23 Å / Num. obs: 136027 / % possible obs: 89.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.84
Reflection shellResolution: 0.94→0.99 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.98 / % possible all: 54.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5phasing
SHELXL-97phasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLS

1nls


Resolution: 0.94→33.23 Å / Num. parameters: 19691 / Num. restraintsaints: 24823 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.142 6827 5 %RANDOM
obs0.12 -89.22 %-
all-136001 --
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 1752.31 / Occupancy sum non hydrogen: 2084.35
Refinement stepCycle: LAST / Resolution: 0.94→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 287 2098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0359
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.135
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.072
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.111

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