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- PDB-5z6d: Crystal structure of Abundant Perithecial Protein (APP) from Neur... -

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Basic information

Entry
Database: PDB / ID: 5z6d
TitleCrystal structure of Abundant Perithecial Protein (APP) from Neurospora crassa
ComponentsDUF1881 domain-containing protein
KeywordsMETAL BINDING PROTEIN / betagamma-crystallin domain / Ig-like domain / Abundant Perithecial Protein
Function / homologyCalcium-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 / cell-cell adhesion / membrane / DUF1881 domain-containing protein
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.6 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF1881 domain-containing protein
B: DUF1881 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)47,7552
Polymers47,7552
Non-polymers00
Water5,657314
1
A: DUF1881 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,8771
Polymers23,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DUF1881 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,8771
Polymers23,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.319, 40.168, 103.542
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23877.252 Da / Num. of mol.: 2 / Mutation: T121M
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: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7RY31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20-25% v/v PEG MME 550, 10-30mM CaCl2, 100mM Bis-Tris, pH 5.5-6.5
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 45708 / % possible obs: 91.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 6 / Num. unique obs: 3831 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.6→23.031 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2289 2316 5.07 %
Rwork0.1837 --
obs0.1859 45669 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 314 3489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073251
X-RAY DIFFRACTIONf_angle_d1.0394414
X-RAY DIFFRACTIONf_dihedral_angle_d12.7461159
X-RAY DIFFRACTIONf_chiral_restr0.041472
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5984-1.6310.313860.24671655X-RAY DIFFRACTION60
1.631-1.66650.29951310.24232480X-RAY DIFFRACTION88
1.6665-1.70530.30461390.23322514X-RAY DIFFRACTION90
1.7053-1.74790.31471360.2322528X-RAY DIFFRACTION90
1.7479-1.79510.32121480.22772505X-RAY DIFFRACTION90
1.7951-1.84790.29561420.21172553X-RAY DIFFRACTION91
1.8479-1.90750.24421360.20062542X-RAY DIFFRACTION91
1.9075-1.97570.24921420.19742587X-RAY DIFFRACTION92
1.9757-2.05470.23531310.19892589X-RAY DIFFRACTION93
2.0547-2.14820.25251250.19232638X-RAY DIFFRACTION93
2.1482-2.26140.23441560.19082649X-RAY DIFFRACTION94
2.2614-2.40290.23741410.18972640X-RAY DIFFRACTION94
2.4029-2.58820.24641400.20132682X-RAY DIFFRACTION95
2.5882-2.84820.27081520.20242710X-RAY DIFFRACTION96
2.8482-3.25940.22791230.18042699X-RAY DIFFRACTION95
3.2594-4.10270.19451390.15492640X-RAY DIFFRACTION92
4.1027-23.03340.17051490.15362742X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -2.9525 Å / Origin y: 30.5365 Å / Origin z: 25.8341 Å
111213212223313233
T0.1369 Å2-0.0121 Å20.0289 Å2-0.1147 Å2-0.004 Å2--0.1727 Å2
L0.546 °2-0.0813 °20.7831 °2-0.095 °20.0162 °2--1.8956 °2
S-0.0312 Å °-0.0454 Å °-0.0585 Å °-0.0169 Å °0.0095 Å °-0.0204 Å °-0.057 Å °-0.1387 Å °0.0233 Å °
Refinement TLS groupSelection details: all

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