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- PDB-4p99: Ca2+-stabilized adhesin helps an Antarctic bacterium reach out an... -

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Basic information

Entry
Database: PDB / ID: 4p99
TitleCa2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice
ComponentsMpAFP_RII tetra-tandemer
KeywordsUNKNOWN FUNCTION / Ca2+-dependent / bacterial Ig-like fold / ice-binding adhesin / extender domain
Function / homologyImmunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / MpAFP_RII tetra-tandemer
Function and homology information
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsGuo, S. / Vance, D.R.T. / Campbell, R.L. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)394878 Canada
CitationJournal: Biosci.Rep. / Year: 2014
Title: Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.
Authors: Vance, T.D. / Olijve, L.L. / Campbell, R.L. / Voets, I.K. / Davies, P.L. / Guo, S.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jan 8, 2020Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: MpAFP_RII tetra-tandemer
B: MpAFP_RII tetra-tandemer
C: MpAFP_RII tetra-tandemer
D: MpAFP_RII tetra-tandemer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,378156
Polymers170,4804
Non-polymers7,898152
Water32,4991804
1
A: MpAFP_RII tetra-tandemer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,24336
Polymers42,6201
Non-polymers1,62335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MpAFP_RII tetra-tandemer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,55341
Polymers42,6201
Non-polymers1,93340
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MpAFP_RII tetra-tandemer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,08843
Polymers42,6201
Non-polymers2,46842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MpAFP_RII tetra-tandemer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,49536
Polymers42,6201
Non-polymers1,87535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.464, 47.469, 191.161
Angle α, β, γ (deg.)90.04, 90.01, 90.02
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein
MpAFP_RII tetra-tandemer


Mass: 42620.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 / References: UniProt: A0A075B5G5*PLUS
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1953 molecules

#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 104 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1804 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.2 M calcium chloride, 0.1 M MES (pH 6) and 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 148953

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.8→47.469 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 7473 5.02 %
Rwork0.2205 --
obs0.2223 148953 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11272 0 348 1804 13424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01811581
X-RAY DIFFRACTIONf_angle_d1.44315911
X-RAY DIFFRACTIONf_dihedral_angle_d14.7593672
X-RAY DIFFRACTIONf_chiral_restr0.0942127
X-RAY DIFFRACTIONf_plane_restr0.0062101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82060.36882430.34094357X-RAY DIFFRACTION86
1.8206-1.8420.35392150.30084480X-RAY DIFFRACTION95
1.842-1.86450.32032380.29744706X-RAY DIFFRACTION95
1.8645-1.88810.35192400.29254664X-RAY DIFFRACTION95
1.8881-1.91290.3082390.28924684X-RAY DIFFRACTION95
1.9129-1.93910.32082360.27414557X-RAY DIFFRACTION95
1.9391-1.96680.29412710.25584822X-RAY DIFFRACTION95
1.9668-1.99620.2642200.24444597X-RAY DIFFRACTION96
1.9962-2.02740.28972500.24154724X-RAY DIFFRACTION96
2.0274-2.06060.26442560.24114678X-RAY DIFFRACTION96
2.0606-2.09610.26822500.23454676X-RAY DIFFRACTION96
2.0961-2.13420.28852550.2334639X-RAY DIFFRACTION96
2.1342-2.17530.25762330.22534840X-RAY DIFFRACTION96
2.1753-2.21970.2712700.22384590X-RAY DIFFRACTION96
2.2197-2.2680.2792250.23044798X-RAY DIFFRACTION96
2.268-2.32070.28882530.22554684X-RAY DIFFRACTION96
2.3207-2.37880.2882390.22264824X-RAY DIFFRACTION97
2.3788-2.44310.28092280.21574628X-RAY DIFFRACTION97
2.4431-2.5150.26652920.21654812X-RAY DIFFRACTION97
2.515-2.59610.24712640.2134724X-RAY DIFFRACTION97
2.5961-2.68890.26642600.21464712X-RAY DIFFRACTION97
2.6889-2.79660.25192520.21344927X-RAY DIFFRACTION98
2.7966-2.92380.2492330.20584691X-RAY DIFFRACTION98
2.9238-3.07790.26922510.20644746X-RAY DIFFRACTION98
3.0779-3.27070.21352490.19874768X-RAY DIFFRACTION98
3.2707-3.52320.22232620.19184841X-RAY DIFFRACTION98
3.5232-3.87760.24042740.19994774X-RAY DIFFRACTION99
3.8776-4.43830.21622720.1974849X-RAY DIFFRACTION99
4.4383-5.59040.232620.20134853X-RAY DIFFRACTION99
5.5904-47.48550.23582410.22314835X-RAY DIFFRACTION99
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)
10.1544-0.06621.23860.7751-0.53334.91910.0517-0.0316-0.05090.08090.01250.06380.2203-0.2873-0.02990.0991-0.01380.01010.18420.00530.1348-9.2384-24.551430.5718
21.326-0.1814-0.01680.1552-1.38422.65520.07360.0602-0.0989-0.11860.03610.07070.5712-0.0717-0.06070.2708-0.005-0.02360.1334-0.00750.1551-11.8789-24.4077-17.701
30.4693-0.094-1.09680.97320.33644.38890.0485-0.02780.1110.04050.0429-0.0951-0.17840.2525-0.08220.0807-0.02240.00120.1523-0.00340.1333-12.6923-24.7444-65.3162
41.37570.04070.120.79251.02172.86890.0263-0.02680.108-0.11490.0729-0.052-0.49090.135-0.07030.2506-0.0090.01340.1527-0.00520.1493-10.1517-25.096-112.5081
50.527-0.0969-0.28910.224-0.89845.02620.0157-0.06550.0020.03540.02890.0717-0.2783-0.1275-0.04920.17660.02-0.00010.097-0.00390.1386-34.606-2.810178.3439
60.3575-0.0863-0.79991.2997-0.41982.4760.0420.07330.0129-0.09590.07750.0967-0.0637-0.5238-0.07030.15840.0039-0.00840.28420.00990.1501-34.3835-0.044630.3901
70.5657-0.14390.35120.64741.52825.0990.0092-0.068-0.04180.01920.0274-0.04670.3130.1512-0.02420.16090.0216-0.00220.12870.00420.1483-34.90720.7078-17.7412
80.55290.12221.24881.05570.39582.16050.05960.1399-0.0234-0.03350.0909-0.04880.13780.6178-0.08890.15870.01290.01010.294-0.02780.1541-35.1129-1.6349-65.2464
91.1630.1663-1.09790.5592-0.57243.62380.0129-0.03240.05440.05740.03080.05680.0518-0.0306-0.03880.1540.0055-0.0060.1142-0.00350.1608-11.7389-0.9843-56.0147
100.308-0.1637-0.79281.2951.21523.93080.0568-0.03920.01780.00480.0443-0.0617-0.11020.0122-0.10740.09740.008-0.00190.14370.00020.1616-11.2244-0.3684-8.5581
111.00480.21670.92180.71230.56013.93940.0181-0.0159-0.0530.03320.0604-0.0495-0.00080.0841-0.06820.13410.00450.01050.1138-0.00640.1642-10.3205-0.799439.539
120.5025-0.39780.61410.7094-1.04073.31890.0727-0.0036-0.03920.00690.03260.05780.06330.0139-0.08280.1258-0.0056-0.01080.1217-0.01430.1573-10.8458-1.71387.3726
130.7499-0.0386-0.69280.471-0.32874.28270.0398-0.0646-0.0014-0.03510.00920.03070.12230.0272-0.04890.08190.0122-0.00250.21740.00240.1394-32.8558-25.2467-89.7332
140.75120.0048-0.34380.56420.54513.89160.01370.06620.03980.04990.0105-0.00570.026-0.1953-0.00730.2210.0090.01940.09680.00970.1412-35.4791-26.5181-41.9529
150.3284-0.09480.33160.3170.41223.71690.05-0.12850.06030.0103-0.0248-0.0228-0.1047-0.0308-0.02220.0903-0.0072-0.00760.2061-0.00260.1355-36.5915-24.09275.7475
160.6581-0.0560.79210.8179-0.27774.1320.01270.0097-0.01930.05240.01840.00810.01290.1756-0.02810.19190.009-0.00280.08640.00180.1286-34.0688-22.846153.4086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:104)
2X-RAY DIFFRACTION2(chain A and resid 105:210)
3X-RAY DIFFRACTION3(chain A and resid 211:312)
4X-RAY DIFFRACTION4(chain A and resid 313:416)
5X-RAY DIFFRACTION5(chain B and resid 2:104)
6X-RAY DIFFRACTION6(chain B and resid 105:210)
7X-RAY DIFFRACTION7(chain B and resid 211:313)
8X-RAY DIFFRACTION8(chain B and resid 314:416)
9X-RAY DIFFRACTION9(chain C and resid 2:103)
10X-RAY DIFFRACTION10(chain C and resid 104:208)
11X-RAY DIFFRACTION11(chain C and resid 209:312)
12X-RAY DIFFRACTION12(chain C and resid 313:416)
13X-RAY DIFFRACTION13(chain D and resid 2:104)
14X-RAY DIFFRACTION14(chain D and resid 105:209)
15X-RAY DIFFRACTION15(chain D and resid 210:312)
16X-RAY DIFFRACTION16(chain D and resid 313:416)

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