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- PDB-3p4g: X-ray crystal structure of a hyperactive, Ca2+-dependent, beta-he... -

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Basic information

Entry
Database: PDB / ID: 3p4g
TitleX-ray crystal structure of a hyperactive, Ca2+-dependent, beta-helical antifreeze protein from an Antarctic bacterium
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / Right-handed Ca2+-binding beta-helix
Function / homology
Function and homology information


Pectate Lyase C-like - #160 / Cadherin-like domain / : / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / Serralysin-like metalloprotease, C-terminal / Pectate Lyase C-like / 3 Solenoid ...Pectate Lyase C-like - #160 / Cadherin-like domain / : / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / Serralysin-like metalloprotease, C-terminal / Pectate Lyase C-like / 3 Solenoid / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGarnham, C.P. / Campbell, R.L. / Davies, P.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Anchored clathrate waters bind antifreeze proteins to ice.
Authors: Garnham, C.P. / Campbell, R.L. / Davies, P.L.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein
B: Antifreeze protein
C: Antifreeze protein
D: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,73462
Polymers133,4354
Non-polymers2,29958
Water20,4111133
1
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,95317
Polymers33,3591
Non-polymers59416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,96316
Polymers33,3591
Non-polymers60415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,93915
Polymers33,3591
Non-polymers58014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,88014
Polymers33,3591
Non-polymers52113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.500, 70.780, 84.250
Angle α, β, γ (deg.)99.06, 92.30, 97.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Antifreeze protein /


Mass: 33358.715 Da / Num. of mol.: 4 / Fragment: unp residues 997-1318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Gene: MpAFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: A1YIY3
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1133 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 10% PEG 8000, 400 mM MgAcetate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.6 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.7→34.6 Å / Num. all: 142852 / Num. obs: 135568 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.088
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.7 / Num. unique all: 18711 / % possible all: 89.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.06 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20022 6803 5 %RANDOM
Rwork0.16363 ---
obs0.16547 128766 94.9 %-
all-142852 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.22 Å2-0.03 Å2
2--0 Å2-0.84 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8879 0 64 1133 10076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0219162
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.92912521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59251292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.21927.263464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9051520
X-RAY DIFFRACTIONr_chiral_restr0.1770.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027220
X-RAY DIFFRACTIONr_mcbond_it1.21.56071
X-RAY DIFFRACTIONr_mcangle_it1.85229699
X-RAY DIFFRACTIONr_scbond_it3.23233091
X-RAY DIFFRACTIONr_scangle_it4.9264.52789
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 418 -
Rwork0.28 8521 -
obs--84.2 %
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)
10.1354-0.2097-0.31320.78480.54021.21970.0418-0.08740.0659-0.14940.0914-0.1882-0.19730.2054-0.13320.0484-0.02620.0340.0701-0.02340.101117.0935-28.979-6.4723
20.4956-0.076-0.30080.58820.44730.93220.01470.0462-0.02290.0171-0.03350.0633-0.0024-0.10790.01890.0097-0.0021-0.01590.02660.01780.05692.1629-59.4151-27.4204
30.7147-0.2548-0.5630.44160.41031.2389-0.0216-0.1735-0.03340.09980.0825-0.05080.03880.2248-0.06080.0410.0035-0.03990.08960.01730.070125.7558-62.3395-14.5197
40.4625-0.09880.17460.54690.30340.67570.00440.04520.00820.0010.0120.11170.0548-0.019-0.01640.0924-0.00420.01560.0390.04870.09-10.0672-25.0754-28.1147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C21 - 321
2X-RAY DIFFRACTION2A23 - 323
3X-RAY DIFFRACTION3B8 - 320
4X-RAY DIFFRACTION4D9 - 320

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