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- PDB-5z6e: Crystal structure of a beta gamma-crystallin domain of Abundant P... -

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Basic information

Entry
Database: PDB / ID: 5z6e
TitleCrystal structure of a beta gamma-crystallin domain of Abundant Perithecial Protein (APP) from Neurospora crassa in the Ca2+-bound form
ComponentsDUF1881 domain-containing protein
KeywordsMETAL BINDING PROTEIN / beta gamma-crystallin domain / Abundant Perithecial Protein / Calcium-binding protein
Function / homology
Function and homology information


cell-cell adhesion / membrane
Similarity search - Function
Calcium-dependent cell adhesion molecule 1, membrane-binding domain / Calcium-dependent cell adhesion molecule, C-terminal domain superfamily / Membrane binding / Calcium-dependent cell adhesion molecule, N-terminal / Beta/Gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
: / DUF1881 domain-containing protein
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.864 Å
AuthorsSrivastava, S.S. / Sankaranarayanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research India
CitationJournal: Mol.Microbiol. / Year: 2018
Title: Interface interactions between beta gamma-crystallin domain and Ig-like domain render Ca2+-binding site inoperative in abundant perithecial protein of Neurospora crassa.
Authors: Swaroop Srivastava, S. / Raman, R. / Kiran, U. / Garg, R. / Chadalawada, S. / Pawar, A.D. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF1881 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2353
Polymers11,1561
Non-polymers792
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-10 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.951, 48.951, 81.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DUF1881 domain-containing protein / Abundant Perithecial Protein / APP


Mass: 11156.263 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: app, NCU04533 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7RY31
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG MME 5000, 0.1M KCl, 0.1M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 9833 / % possible obs: 98.2 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.4
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.256 / Num. unique obs: 830 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDF

1hdf


Resolution: 1.864→23.449 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.33
RfactorNum. reflection% reflection
Rfree0.2013 469 4.78 %
Rwork0.1588 --
obs0.1607 9811 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.864→23.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 2 111 815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007719
X-RAY DIFFRACTIONf_angle_d1.061977
X-RAY DIFFRACTIONf_dihedral_angle_d11.415251
X-RAY DIFFRACTIONf_chiral_restr0.042104
X-RAY DIFFRACTIONf_plane_restr0.004128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8639-2.13340.18991600.15382969X-RAY DIFFRACTION96
2.1334-2.68730.22541540.16673105X-RAY DIFFRACTION100
2.6873-23.45120.19231550.15633268X-RAY DIFFRACTION100

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