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- PDB-1yj0: Crystal Structures of Chicken Annexin V in Complex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 1yj0
TitleCrystal Structures of Chicken Annexin V in Complex with Zn2+
ComponentsAnnexin A5
KeywordsPROTEIN AND METAL BINDING PROTEIN / Annexin / membrane binding / matrix vessicle
Function / homology
Function and homology information


Platelet degranulation / negative regulation of coagulation / calcium-dependent phospholipid binding / calcium ion homeostasis / calcium channel complex / sarcolemma / calcium channel activity / vesicle / calcium ion binding / cytoplasm
Similarity search - Function
Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsOrtlund, E.A. / Chai, G. / Genge, B. / Wu, L.N.Y. / Wuthier, R.E. / Lebioda, L.
CitationJournal: Annexins / Year: 2005
Title: Crystal Structures of Chicken Annexin A5 in Complex with Functional Modifiers Ca2+ and Zn2+ Reveal Zn2+ Induced Formation of Non-Planar Assemblies
Authors: Ortlund, E.A. / Chai, G. / Genge, B. / Wu, L.N.Y. / Wuthier, R.E. / Lebioda, L.
History
DepositionJan 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.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_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

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Assembly

Deposited unit
A: Annexin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,01611
Polymers36,1171
Non-polymers89910
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Annexin A5
hetero molecules

A: Annexin A5
hetero molecules

A: Annexin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,04933
Polymers108,3513
Non-polymers2,69830
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area8820 Å2
ΔGint-468 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.593, 106.593, 106.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-508-

SO4

21A-508-

SO4

31A-401-

ZN

41A-645-

HOH

51A-651-

HOH

61A-661-

HOH

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Components

#1: Protein Annexin A5 / / Annexin V / Lipocortin V / Endonexin II / Calphobindin I / CBP-I / Placental anticoagulant protein ...Annexin V / Lipocortin V / Endonexin II / Calphobindin I / CBP-I / Placental anticoagulant protein I / PAP-I / PP4 / Thromboplastin inhibitor / Vascular anticoagulant-alpha / VAC-alpha / Anchorin CII


Mass: 36117.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene ANXA5, ANX5 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P17153
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: Ammonium Sulfate, zinc chloride, HEPES, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorDetector: CCD / Date: Mar 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→43.52 Å / Num. obs: 9102 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 100.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.408 / Num. unique all: 865 / % possible all: 98.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→43.52 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 292344.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 890 10.6 %RANDOM
Rwork0.211 ---
obs0.2111 8401 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.0812 Å2 / ksol: 0.325923 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.95→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 42 64 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 127 9.9 %
Rwork0.319 1155 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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