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- PDB-2xiw: Crystal structure of the Sac7d-derived IgG1-binder C3-C24S -

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Basic information

Entry
Database: PDB / ID: 2xiw
TitleCrystal structure of the Sac7d-derived IgG1-binder C3-C24S
ComponentsDNA-BINDING PROTEIN 7D
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-binding protein 7d
Similarity search - Component
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBellinzoni, M. / Colinet, S. / Behar, G. / Alzari, P.M. / Pecorari, F.
CitationJournal: Protein Eng.Des.Sel. / Year: 2013
Title: Tolerance of the Archaeal Sac7D Scaffold Protein to Alternative Library Designs: Characterization of Anti-Immunoglobulin G Affitins.
Authors: Behar, G. / Bellinzoni, M. / Maillasson, M. / Paillard-Laurance, L. / Alzari, P.M. / He, X. / Mouratou, B. / Pecorari, F.
History
DepositionJul 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references / Structure summary / Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: DNA-BINDING PROTEIN 7D
B: DNA-BINDING PROTEIN 7D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5645
Polymers18,3362
Non-polymers2283
Water3,279182
1
A: DNA-BINDING PROTEIN 7D
B: DNA-BINDING PROTEIN 7D
hetero molecules

A: DNA-BINDING PROTEIN 7D
B: DNA-BINDING PROTEIN 7D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,12710
Polymers36,6724
Non-polymers4556
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5630 Å2
ΔGint-64.8 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.175, 73.175, 57.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-1070-

CL

21B-2073-

HOH

31B-2082-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.71044, 0.63121, 0.31122), (0.70376, 0.63561, 0.31737), (0.00251, 0.4445, -0.89578)
Vector: -64.04092, 31.93723, -0.12374)

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Components

#1: Protein DNA-BINDING PROTEIN 7D / NANOFITIN C3-C24S / 7 KDA DNA-BINDING PROTEIN D / SAC7D


Mass: 9168.037 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): IQ / References: UniProt: P13123
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL STRETCH MRGSHHHHHHGS IS A CLONING ARTIFACT

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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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growDetails: 3.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→31.7 Å / Num. obs: 28098 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 17.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
SHELX-AUTOSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→18.37 Å / Cor.coef. Fo:Fc: 0.9576 / Cor.coef. Fo:Fc free: 0.9524 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.062
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1408 5.01 %RANDOM
Rwork0.1752 ---
obs0.176 28081 97.56 %-
Displacement parametersBiso mean: 22.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.5256 Å20 Å20 Å2
2---0.5256 Å20 Å2
3---1.0512 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.5→18.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 11 182 1235
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011153HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.131561HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d476SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes173HARMONIC5
X-RAY DIFFRACTIONt_it1153HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion13.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion140SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies15HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1491SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.56 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.215 142 5.01 %
Rwork0.1936 2695 -
all0.1946 2837 -
obs--97.56 %
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)
11.04140.87320.02722.09340.11262.26240.0840.01510.07660.1123-0.02390.2130.1122-0.1207-0.06010.0873-0.00440.02970.0266-0.00770.0421-40.17656.55959.2073
21.0245-0.25240.07041.85890.50931.02390.07070.01490.06240.0018-0.0248-0.0017-0.03150.1188-0.0460.0495-0.00960.01770.01580.00150.0203-28.637210.2026-6.6155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2:65
2X-RAY DIFFRACTION2CHAIN B AND RESID 2:68

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