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- PDB-1dm5: ANNEXIN XII E105K HOMOHEXAMER CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1dm5
TitleANNEXIN XII E105K HOMOHEXAMER CRYSTAL STRUCTURE
ComponentsANNEXIN XII E105K MUTANT HOMOHEXAMER
KeywordsUNKNOWN FUNCTION / HOMOHEXAMER / NOVEL PH-DEPENDENT HEXAMERIZATION SWITCH E76 / LOW CALCIUM FORM / MIXED TYPEII/TYPEIII CALCIUM BINDING SITE / E105K EPSILON AMINO GROUP REPLACES INTERMOLECULAR CALCIUM
Function / homology
Function and homology information


calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / calcium ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 ...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 speciesHydra vulgaris (swiftwater hydra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsCartailler, J.P. / Haigler, H.T. / Luecke, H.
CitationJournal: Biochemistry / Year: 2000
Title: Annexin XII E105K crystal structure: identification of a pH-dependent switch for mutant hexamerization.
Authors: Cartailler, J.P. / Haigler, H.T. / Luecke, H.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2019Group: Data collection / Category: reflns / Item: _reflns.B_iso_Wilson_estimate
Revision 1.6Feb 7, 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_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.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 / _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_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

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Assembly

Deposited unit
A: ANNEXIN XII E105K MUTANT HOMOHEXAMER
B: ANNEXIN XII E105K MUTANT HOMOHEXAMER
C: ANNEXIN XII E105K MUTANT HOMOHEXAMER
D: ANNEXIN XII E105K MUTANT HOMOHEXAMER
E: ANNEXIN XII E105K MUTANT HOMOHEXAMER
F: ANNEXIN XII E105K MUTANT HOMOHEXAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,58817
Polymers210,1476
Non-polymers44111
Water16,682926
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-148 kcal/mol
Surface area73720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.943, 162.544, 188.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ANNEXIN XII E105K MUTANT HOMOHEXAMER


Mass: 35024.539 Da / Num. of mol.: 6 / Mutation: E105K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Production host: Escherichia coli (E. coli) / References: UniProt: P26256
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M AMMONIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6 80 % 2-METHYL-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium citrate1reservoir
480 %2-methylpentanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 969367 / Num. obs: 156877 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.295 / % possible all: 75.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 969367
Reflection shell
*PLUS
% possible obs: 93.8 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.93→10 Å / σ(F): 4 / σ(I): 0 / Stereochemistry target values: SHELXL
Details: -WATERS WERE ADDED ONCE THE RFREE DROPPED BELOW 30% -NCS RESTRAINTS WERE USED UNTIL CONVERGENCE AT RFREE=32% -NCS RESTRAINTS THEN RELAXED TO ALLOW LOOP INDEPENDENT LOOP MOTIONS IN NCS COPIES ...Details: -WATERS WERE ADDED ONCE THE RFREE DROPPED BELOW 30% -NCS RESTRAINTS WERE USED UNTIL CONVERGENCE AT RFREE=32% -NCS RESTRAINTS THEN RELAXED TO ALLOW LOOP INDEPENDENT LOOP MOTIONS IN NCS COPIES -RANDOM DISPLACEMENT OF ATOMIC POSITIONS AND B-VALUES FROM THEIR CURRENT VALUES (MAIN-"KICKING") WAS USED TO REDUCE MODEL BIAS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 7790 -5% RANDOMLY SELECTED REFLECTIONS
Rwork0.208 ---
all0.236 156921 --
obs0.215 155796 92.5 %-
Refinement stepCycle: LAST / Resolution: 1.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 0 11 926 15709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d1.5
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 4 / Rfactor obs: 0.208 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.5

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