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- PDB-4x9p: Crystal structure of bovine Annexin A2 -

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Basic information

Entry
Database: PDB / ID: 4x9p
TitleCrystal structure of bovine Annexin A2
ComponentsAnnexin A2
KeywordsCALCIUM BINDING PROTEIN / annexin / calcium binding
Function / homology
Function and homology information


extracellular membrane-bounded organelle / small GTPase binding => GO:0031267 / biomineral tissue development / phospholipase A2 inhibitor activity / calcium-dependent phospholipid binding / calcium ion import / virion binding / Neutrophil degranulation / phosphatidylserine binding / basement membrane ...extracellular membrane-bounded organelle / small GTPase binding => GO:0031267 / biomineral tissue development / phospholipase A2 inhibitor activity / calcium-dependent phospholipid binding / calcium ion import / virion binding / Neutrophil degranulation / phosphatidylserine binding / basement membrane / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / calcium ion transmembrane transport / calcium channel activity / melanosome / protease binding / vesicle / endosome / intracellular membrane-bounded organelle / calcium ion binding / extracellular space / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsShumilin, I.A. / Hollas, H. / Vedeler, A. / Kretsinger, R.H.
CitationJournal: Biochem. Pharmacol. / Year: 2015
Title: The native structure of annexin A2 peptides in hydrophilic environment determines their anti-angiogenic effects.
Authors: Raddum, A.M. / Hollas, H. / Shumilin, I.A. / Henklein, P. / Kretsinger, R. / Fossen, T. / Vedeler, A.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Structure summary
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Apr 29, 2015Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _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_symmetry / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1415
Polymers38,9851
Non-polymers1564
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-31 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.315, 63.274, 117.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Annexin A2 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / ...Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 38985.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ANXA2, ANX2 / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04272
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Reservoir buffer: 30% PEG 4000, 0.1 M Na acetate, 0.2 M ammonium acetate. The drop consisted of 0.5 mkl of 2.3 mg/ml protein solution + 0.5 mkl of reservoir buffer supplemented with 20 mkM Ca2+ and 1 mM Mg2+.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97901 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 14, 2007
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Number: 168541 / Rmerge(I) obs: 0.048 / Χ2: 0.88 / D res high: 2.01 Å / D res low: 50 Å / Num. obs: 24564 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.335010.0250.9676.3
3.444.3310.0321.126.7
33.4410.041.0126.9
2.73310.0560.9347
2.532.7310.0790.8627
2.382.5310.090.7487.1
2.262.3810.1220.7377.1
2.172.2610.1610.817.1
2.082.1710.1990.7457.1
2.012.0810.2760.8656.4
ReflectionResolution: 2.01→50 Å / Num. obs: 24564 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Χ2: 0.879 / Net I/av σ(I): 37.608 / Net I/σ(I): 12.1 / Num. measured all: 168541
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.01-2.086.40.2765.924180.86599.1
2.08-2.177.10.19923880.74599.8
2.17-2.267.10.16124210.8199.9
2.26-2.387.10.12224070.73799.8
2.38-2.537.10.0924630.748100
2.53-2.7370.07924190.86299.9
2.73-370.05624570.93499.8
3-3.446.90.0424651.01299.9
3.44-4.336.70.03225021.12100
4.33-506.30.02526240.96798.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XJL

1xjl


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2048 / WRfactor Rwork: 0.1536 / FOM work R set: 0.8636 / SU B: 6.663 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1551 / SU Rfree: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1256 5.1 %RANDOM
Rwork0.1565 23260 --
obs0.1592 23260 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.03 Å2 / Biso mean: 39.063 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--1.19 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 4 267 2796
Biso mean--54.27 44.66 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022576
X-RAY DIFFRACTIONr_bond_other_d0.0010.022507
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9823462
X-RAY DIFFRACTIONr_angle_other_deg0.83235790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98624.553123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38315514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7311519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_mcbond_it2.2242.1891260
X-RAY DIFFRACTIONr_mcbond_other2.2242.1881259
X-RAY DIFFRACTIONr_mcangle_it3.4153.2651573
LS refinement shellResolution: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 91 -
Rwork0.172 1635 -
all-1726 -
obs--97.4 %
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)
11.9799-0.0646-1.70120.8723-0.5782.69960.038-0.0585-0.01920.020.1303-0.0218-0.0366-0.1737-0.16830.0036-0.0075-0.0210.21210.05320.1997-28.2647.17254.188
21.2834-0.6943-0.9690.44490.22672.16440.24510.3727-0.2291-0.1384-0.20460.1676-0.1646-0.4687-0.04050.050.0586-0.04710.3107-0.05280.173-27.09248.16131.482
31.2917-1.092-0.42233.33690.54611.03320.00880.1477-0.0435-0.1829-0.0369-0.1714-0.1537-0.10910.0280.04130.01170.02270.1591-0.03570.126-5.45640.42916.226
41.2956-0.3465-0.49050.9834-0.1950.97110.1087-0.02780.0308-0.0422-0.07350.0207-0.00430.1084-0.03510.03-0.00360.01130.16160.00130.1447-10.38452.34941.863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 76
2X-RAY DIFFRACTION2A77 - 184
3X-RAY DIFFRACTION3A185 - 264
4X-RAY DIFFRACTION4A265 - 339

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