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- PDB-1a4p: P11 (S100A10), LIGAND OF ANNEXIN II -

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Basic information

Entry
Database: PDB / ID: 1a4p
TitleP11 (S100A10), LIGAND OF ANNEXIN II
ComponentsS100A10
KeywordsCALCIUM/PHOSPHOLIPID BINDING PROTEIN / S100 FAMILY / EF-HAND PROTEIN / LIGAND OF ANNEXIN II / CALCIUM-PHOSPHOLIPID BINDING PROTEIN complex
Function / homology
Function and homology information


AnxA2-p11 complex / membrane raft assembly / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / vesicle budding from membrane / plasma membrane protein complex / Dissolution of Fibrin Clot / positive regulation of exocytosis / positive regulation of GTPase activity / positive regulation of focal adhesion assembly ...AnxA2-p11 complex / membrane raft assembly / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / vesicle budding from membrane / plasma membrane protein complex / Dissolution of Fibrin Clot / positive regulation of exocytosis / positive regulation of GTPase activity / positive regulation of focal adhesion assembly / regulation of neurogenesis / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / protein localization to plasma membrane / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / : / transmembrane transporter binding / calcium ion binding / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Protein S100-A10 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsRety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Russo-Marie, F. / Lewit-Bentley, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of a complex of p11 with the annexin II N-terminal peptide.
Authors: Rety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Tabaries, S. / Russo-Marie, F. / Lewit-Bentley, A.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: S100A10
B: S100A10


Theoretical massNumber of molelcules
Total (without water)22,1782
Polymers22,1782
Non-polymers00
Water1,13563
1
A: S100A10
B: S100A10

A: S100A10
B: S100A10

A: S100A10
B: S100A10

A: S100A10
B: S100A10


Theoretical massNumber of molelcules
Total (without water)88,7128
Polymers88,7128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area16650 Å2
ΔGint-174 kcal/mol
Surface area38210 Å2
MethodPISA
2
A: S100A10

A: S100A10

A: S100A10

A: S100A10

B: S100A10

B: S100A10

B: S100A10

B: S100A10


Theoretical massNumber of molelcules
Total (without water)88,7128
Polymers88,7128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation3_856-x+3,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_666x+1,-y+1,-z+11
Buried area18200 Å2
ΔGint-184 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.750, 80.750, 95.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.85907, -0.47311, -0.19537), (0.47068, -0.88014, 0.06174), (-0.20116, -0.03892, 0.97878)
Vector: 146.39342, 87.33656, 15.64443)

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Components

#1: Protein S100A10 / P11 / CALPACTIN LIGHT CHAIN


Mass: 11088.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60903
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 15 MG/ML PROTEIN WERE CRYSTALLIZED BY VAPOR DIFFUSION AGAINST 20% PEG 4000, 10% 2-PROPANOL, 100MM HEPES, PH=7.5, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: drop:reservoir=1:1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMNa acetate1drop
2250 mM1dropNaCl
31 mM1dropNaN3
41 mMdithiothreitol1drop
520 %PEG40001reservoir
610 %2-propanol1reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.37
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 18, 1997 / Details: FOCUSSING MONOCHROMATOR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 2.25→62 Å / Num. obs: 10769 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Rsym value: 0.047 / Net I/σ(I): 14.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.168 / % possible all: 97.1
Reflection
*PLUS
Num. obs: 10957 / Num. measured all: 67368 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.168

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1075 10 %RANDOM
Rwork0.227 ---
obs0.246 9679 98.4 %-
Displacement parametersBiso mean: 36.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 0 63 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9112
X-RAY DIFFRACTIONp_mcangle_it3.0813
X-RAY DIFFRACTIONp_scbond_it22
X-RAY DIFFRACTIONp_scangle_it3.193
X-RAY DIFFRACTIONp_plane_restr0.0090.015
X-RAY DIFFRACTIONp_chiral_restr0.1830.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2120.3
X-RAY DIFFRACTIONp_planar_tor1.77
X-RAY DIFFRACTIONp_staggered_tor23.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.320
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.246 / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS

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