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- PDB-4rgh: Human DNA Damage-Inducible Protein: From Protein Chemistry and 3D... -

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Basic information

Entry
Database: PDB / ID: 4rgh
TitleHuman DNA Damage-Inducible Protein: From Protein Chemistry and 3D Structure to Deciphering its Cellular Role
ComponentsProtein DDI1 homolog 2
KeywordsHYDROLASE / retroviral protease-like domain / putative proteolytical activity
Function / homology
Function and homology information


regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / ubiquitin binding / regulation of protein stability / protein processing / chromosome / aspartic-type endopeptidase activity / nucleoplasm ...regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / ubiquitin binding / regulation of protein stability / protein processing / chromosome / aspartic-type endopeptidase activity / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Aspartic peptidase domain superfamily / Ubiquitin-like domain superfamily ...DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Aspartic peptidase domain superfamily / Ubiquitin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein DDI1 homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBrynda, J. / Grantz Saskova, K.
CitationJournal: To be Published
Title: Human DNA Damage-Inducible Protein: From Protein Chemistry and 3D Structure to Deciphering its Cellular Role
Authors: Siva, M. / Svoboda, M. / Veverka, V. / Brynda, J. / Trempe, J.-F. / Kozisek, M. / Fleisigova, I. / Belza, J. / Konvalinka, J. / Grantz Saskova, K.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Protein DDI1 homolog 2
B: Protein DDI1 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1034
Polymers38,0322
Non-polymers712
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-21 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.870, 86.400, 52.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 200 - 327 / Label seq-ID: 41 - 168

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Protein DDI1 homolog 2


Mass: 19015.891 Da / Num. of mol.: 2
Fragment: Retroviral protease-like domain, UNP residues 212-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDI2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q5TDH0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M amonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91573 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91573 Å / Relative weight: 1
ReflectionResolution: 1.9→87.09 Å / Num. obs: 21413 / % possible obs: 87.2 % / Redundancy: 4.6 % / Rsym value: 0.09 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-24.70.3262.21147524600.32669.7
2-2.124.70.25331320028180.25384.4
2.12-2.274.70.2273.21197825580.22781.7
2.27-2.454.70.1614.51369329240.161100
2.45-2.694.70.1265.71102623610.12686.8
2.69-34.70.0838.11135924280.08398.8
3-3.474.60.0619937220170.06191.6
3.47-4.254.60.0628.8689315020.06280.6
4.25-6.014.50.0578.8664814770.057100
6.01-26.4414.20.03912.236198680.03998.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2448 / WRfactor Rwork: 0.2009 / FOM work R set: 0.8237 / SU B: 3.917 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1711 / SU Rfree: 0.1633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1042 4.9 %RANDOM
Rwork0.2076 ---
obs0.2098 20350 87.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.55 Å2 / Biso mean: 21.765 Å2 / Biso min: 14.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--2.27 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 2 86 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191980
X-RAY DIFFRACTIONr_bond_other_d0.0050.021353
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9752679
X-RAY DIFFRACTIONr_angle_other_deg0.94933338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40924.81581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6641512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1555 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.380.5
MEDIUM THERMAL2.872
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 62 -
Rwork0.395 927 -
all-989 -
obs--58.56 %

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