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- PDB-4mdv: Crystal structure of calcium-bound annexin (Sm)1 -

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Basic information

Entry
Database: PDB / ID: 4mdv
TitleCrystal structure of calcium-bound annexin (Sm)1
ComponentsAnnexin
KeywordsMETAL BINDING PROTEIN / annexin / calcium-binding protein
Function / homology
Function and homology information


calcium-dependent phospholipid binding / calcium ion binding / identical protein binding
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 speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHofmann, A.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structure and immunological properties of the first annexin from Schistosoma mansoni: insights into the structural integrity of the schistosomal tegument.
Authors: Leow, C.Y. / Willis, C. / Osman, A. / Mason, L. / Simon, A. / Smith, B.J. / Gasser, R.B. / Jones, M.K. / Hofmann, A.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_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

Downloads & links

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Assembly

Deposited unit
A: Annexin
B: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,15215
Polymers85,6312
Non-polymers52113
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-144 kcal/mol
Surface area30710 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-120 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.822, 88.486, 68.465
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and backbone
211chain B and backbone

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Components

#1: Protein Annexin /


Mass: 42815.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: annexin (Sm)1, Smp_074150.1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4QH88
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 12.5% PEG2000, 50 mM TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.3378 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3378 Å / Relative weight: 1
ReflectionResolution: 2.5→24.1 Å / Num. obs: 26180 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rsym value: 0.041
Reflection shellHighest resolution: 2.5 Å / Redundancy: 3.6 % / Rsym value: 0.386 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDU

4mdu


Resolution: 2.5→24.1 Å / SU ML: 0.47 / σ(F): 0.98 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2604 5.1 %
Rwork0.1902 --
obs0.1937 24835 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.315 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.786 Å20 Å2-5.6488 Å2
2---3.3565 Å20 Å2
3----3.4294 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 13 117 5744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115791
X-RAY DIFFRACTIONf_angle_d1.1887752
X-RAY DIFFRACTIONf_dihedral_angle_d15.2852208
X-RAY DIFFRACTIONf_chiral_restr0.083877
X-RAY DIFFRACTIONf_plane_restr0.005981
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1396X-RAY DIFFRACTIONPOSITIONAL
12B1396X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54550.36551450.29752446X-RAY DIFFRACTION95
2.5455-2.59440.39751540.32548X-RAY DIFFRACTION100
2.5944-2.64730.42081200.33372539X-RAY DIFFRACTION100
2.6473-2.70480.36131150.26892559X-RAY DIFFRACTION100
2.7048-2.76760.33221450.27982556X-RAY DIFFRACTION100
2.7676-2.83670.35171600.26682576X-RAY DIFFRACTION100
2.8367-2.91330.3821370.24152522X-RAY DIFFRACTION100
2.9133-2.99880.33871340.23752583X-RAY DIFFRACTION100
2.9988-3.09540.36491520.25472548X-RAY DIFFRACTION100
3.0954-3.20580.32871430.24572538X-RAY DIFFRACTION100
3.2058-3.33390.29551550.20542537X-RAY DIFFRACTION100
3.3339-3.48520.28031310.20662594X-RAY DIFFRACTION100
3.4852-3.66830.25621350.19582547X-RAY DIFFRACTION100
3.6683-3.89730.24411210.18182571X-RAY DIFFRACTION100
3.8973-4.19670.21961140.15682597X-RAY DIFFRACTION100
4.1967-4.61640.17851350.13942541X-RAY DIFFRACTION100
4.6164-5.27830.22661310.1412578X-RAY DIFFRACTION100
5.2783-6.62720.21861260.18982551X-RAY DIFFRACTION100
6.6272-24.13330.22051510.16172547X-RAY DIFFRACTION99
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)
10.7071-1.08710.3261.13340.02220.9628-0.0298-0.0431-0.150.0252-0.0190.19440.0607-0.10860.03740.233-0.00180.03190.23720.04720.2933-20.1259-4.709-31.7131
21.263-0.2757-0.27291.061-0.15120.5653-0.07630.0852-0.0908-0.02760.1985-0.069-0.119-0.0303-0.11180.27270.022-0.01190.3146-0.01170.26486.13735.3372-59.97
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 364
2X-RAY DIFFRACTION2chain BB6 - 363

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