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- PDB-2zhj: Crystal Structure Analysis of the Sodium-Bound Annexin A4 at 1.34... -

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Basic information

Entry
Database: PDB / ID: 2zhj
TitleCrystal Structure Analysis of the Sodium-Bound Annexin A4 at 1.34 A resolution
ComponentsAnnexin A4
KeywordsMETAL BINDING PROTEIN / zynogen granule / membrane binding protein / Annexin / Calcium / Calcium/phospholipid-binding
Function / homology
Function and homology information


zymogen granule membrane / negative regulation of interleukin-8 production / vesicle membrane / calcium-dependent phospholipid binding / exocytosis / NF-kappaB binding / Notch signaling pathway / epithelial cell differentiation / calcium-dependent protein binding / nuclear membrane ...zymogen granule membrane / negative regulation of interleukin-8 production / vesicle membrane / calcium-dependent phospholipid binding / exocytosis / NF-kappaB binding / Notch signaling pathway / epithelial cell differentiation / calcium-dependent protein binding / nuclear membrane / calcium ion binding / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / cell surface / identical protein binding / nucleus / plasma membrane / cytoplasm
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
Annexin A4 / Annexin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsButsushita, K. / Ida, K. / Fukuoka, S.-I. / Arii, Y.
CitationJournal: To be Published
Title: Structural Analysis for the Soduim-Dependent Dissociation of Annexin A4: Crystal Structures of Soduim-Bound Annexin A4 at High Resolutions
Authors: Butsushita, K. / Inoue, K. / Ida, K. / Fukuoka, S.-I. / Arii, Y.
History
DepositionFeb 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2543
Polymers36,2081
Non-polymers462
Water7,026390
1
A: Annexin A4
hetero molecules

A: Annexin A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5086
Polymers72,4162
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.427, 39.528, 65.510
Angle α, β, γ (deg.)90.00, 95.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Annexin A4 /


Mass: 36208.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Anxa4 / Plasmid: pGEX3x / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q5U362, UniProt: P55260*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M soduim citrate, 0.5M ammonium sulfate, 0.9M lithium sulfate, pH5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2005
RadiationMonochromator: Triangular Si(111) with an asymmetric angle of 7.8
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 59904 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.2
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.5 / % possible all: 99.5

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANN

1ann


Resolution: 1.35→10 Å / Num. parameters: 25878 / Num. restraintsaints: 30671 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY SHELXL
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3268 5.3 %RANDOM
Rwork0.143 ---
all0.1435 59904 --
obs0.1435 59904 94.7 %-
Displacement parametersBiso mean: 27.635 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2872
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 2 390 2875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0256
X-RAY DIFFRACTIONs_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.091
LS refinement shellResolution: 1.35→1.4 Å
RfactorNum. reflection
Rfree0.201 2874
Rwork0.143 -
obs-54246

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