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- PDB-1aow: ANNEXIN IV -

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Basic information

Entry
Database: PDB / ID: 1aow
TitleANNEXIN IV
ComponentsANNEXIN IV
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / 32.5KD CALELECTRIN / ENDONEXIN I / LIPOCORTIN IV / CHROMOBINDIN IV / PROTEIN II / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex
Function / homology
Function and homology information


chondroitin sulfate binding / chromaffin granule membrane / zymogen granule membrane / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / heparin binding / carbohydrate binding / apical plasma membrane / calcium ion binding ...chondroitin sulfate binding / chromaffin granule membrane / zymogen granule membrane / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / heparin binding / carbohydrate binding / apical plasma membrane / calcium ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Annexin A4 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A4 / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZanotti, G. / Malpeli, G. / Gliubich, F. / Folli, C. / Stoppini, M. / Olivi, L. / Savoia, A. / Berni, R.
CitationJournal: Biochem.J. / Year: 1998
Title: Structure of the trigonal crystal form of bovine annexin IV.
Authors: Zanotti, G. / Malpeli, G. / Gliubich, F. / Folli, C. / Stoppini, M. / Olivi, L. / Savoia, A. / Berni, R.
History
DepositionJul 11, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANNEXIN IV


Theoretical massNumber of molelcules
Total (without water)35,0061
Polymers35,0061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.560, 118.560, 82.233
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ANNEXIN IV / 32.5 KD CALELECTRIN / ENDONEXIN I


Mass: 35005.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: KIDNEY / References: UniProt: P13214

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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: 3.37 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: SITTING DROP, FROM A PROTEIN SOLUTION 10 MG/ML, IN THE PRESENCE OF 1.4 M AMMONIUM SULFATE, 10 MM BETA-MERCAPTOETHANOL, PH=5.0, vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 Mammonium sulfate1drop
350 mMTris-HCl1drop
41.4 Mammonium sulfate1reservoir
510 mM2-mercaptoethanol1reservoir
60.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.3
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 8114 / % possible obs: 95 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 36
Reflection shellResolution: 2.99→3.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 10 / Rsym value: 0.07 / % possible all: 75.3
Reflection
*PLUS
Highest resolution: 2.99 Å / Lowest resolution: 50 Å / % possible obs: 93 %
Reflection shell
*PLUS
Lowest resolution: 3.5 Å / % possible obs: 87 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
MARSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANN

1ann


Resolution: 3→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -11 %RANDOM
Rwork0.19 ---
obs0.19 7517 95 %-
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 0 0 3039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.99 Å / Lowest resolution: 7 Å / Num. reflection obs: 6717 / Num. reflection Rfree: 800
Solvent computation
*PLUS
Displacement parameters
*PLUS

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