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- PDB-3gxy: Crystal structure of cyanovirin-n complexed to a synthetic hexama... -

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Basic information

Entry
Database: PDB / ID: 3gxy
TitleCrystal structure of cyanovirin-n complexed to a synthetic hexamannoside
ComponentsCyanovirin-N
KeywordsANTIVIRAL PROTEIN / CYANOVIRIN-N / HIV-INACTIVATING / DOMAIN-SWAPPING / GP120 / MAN-9 / OLIGOSACCHARIDE / Disulfide bond / Protein synthesis inhibitor
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBotos, I. / O'Keefe, B.R. / Shenoy, S.R. / Seeberger, P.H. / Boyd, M.R. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structures of the complexes of a potent anti-HIV protein cyanovirin-n and high mannose oligosaccharides
Authors: Botos, I. / O'Keefe, B.R. / Shenoy, S.R. / Cartner, L.K. / Ratner, D.M. / Seeberger, P.H. / Boyd, M.R. / Wlodawer, A.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMay 5, 2009ID: 1M5J
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Cyanovirin-N
B: Cyanovirin-N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4256
Polymers22,0442
Non-polymers1,3814
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.352, 61.352, 147.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cyanovirin-N / CV-N


Mass: 11022.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-pentyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 574.571 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122h-1a_1-5_1*OCCCCC][a1122h-1a_1-5]/1-2-2/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][pentyl]{[(1+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.3
Details: 0.1M CHES, 1M NaCitrate, pH 10.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2001 / Details: mirror
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 11728 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EZM

3ezm


Resolution: 2.4→19.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.086 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 555 4.8 %RANDOM
Rwork0.20807 ---
obs0.21102 11069 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 92 104 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211658
X-RAY DIFFRACTIONr_angle_refined_deg2.1961.9992249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52626.21674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.397156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021168
X-RAY DIFFRACTIONr_mcbond_it0.7191.5998
X-RAY DIFFRACTIONr_mcangle_it1.38321608
X-RAY DIFFRACTIONr_scbond_it2.3313660
X-RAY DIFFRACTIONr_scangle_it3.7414.5638
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 37 -
Rwork0.384 799 -
obs--100 %
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)
11.61520.75780.24221.82250.51341.30780.0031-0.23430.1010.2515-0.1842-0.00340.0785-0.05470.1810.26020.074-0.03340.3424-0.02870.131424.27637.23126.469
21.38150.4236-0.70322.04740.35271.7639-0.0527-0.2081-0.04820.1312-0.0788-0.22540.16840.20670.13140.24220.1153-0.06180.35450.01690.155629.99735.671125.457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B1 - 101

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