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- PDB-2i7r: conserved domain protein -

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Basic information

Entry
Database: PDB / ID: 2i7r
Titleconserved domain protein
ComponentsConserved domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / structural genomics conserved domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Conserved domain protein / Conserved domain protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDuke, N.E.C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: conserved domain protein
Authors: Duke, N.E.C. / Zhou, M. / Abdullah, J. / Joachimiak, A.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved domain protein
B: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)26,6272
Polymers26,6272
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-27 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.624, 97.624, 55.151
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Conserved domain protein


Mass: 13313.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q97RR3, UniProt: A0A0H2UP77*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.100 M sodium citrate 2.00 M sodium chloride, pH 4.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979321 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 27, 2005 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979321 Å / Relative weight: 1
ReflectionRedundancy: 12.7 % / Av σ(I) over netI: 8.5 / Number: 376937 / Rmerge(I) obs: 0.096 / Χ2: 1.09 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 29639 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745099.310.0381.39713.1
3.764.7499.310.0421.16813.3
3.293.7699.510.0691.34213.5
2.993.2999.310.0991.19513.7
2.772.9999.410.1661.00413.7
2.612.7799.410.2571.01613.7
2.482.6199.410.3111.00513.6
2.372.4899.510.3860.96412.7
2.282.3799.410.4540.8611
2.22.2899.210.4590.8288.6
ReflectionResolution: 2.2→50 Å / Num. obs: 15324 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.096 / Χ2: 1.093 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.459 / Num. unique all: 2952 / Χ2: 0.828 / % possible all: 99.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 50 Å / FOM : 0.417 / FOM acentric: 0.446 / FOM centric: 0 / Reflection: 10503 / Reflection acentric: 9815 / Reflection centric: 688
Phasing MAD setR cullis acentric: 2.05 / R cullis centric: 1 / Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Loc acentric: 0.3 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 9815 / Reflection centric: 688
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
14.81-500.940.60.63616
8.7-14.811.150.70.517438
6.15-8.72.010.60.341054
4.76-6.151.790.60.375979
3.88-4.761.190.40.3118796
3.28-3.881.480.20.11741114
2.84-3.284.30.202383135
2.5-2.848.650.203125156
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se31.2110.9350.3250.1620
2Se31.2870.1850.4150.0730
3Se46.8170.6310.8020.0770
4Se52.8060.3460.0660.1590
5Se36.5630.0250.3250.0760
6Se40.270.0830.3470.1590
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.81-500.4240.6120523616
8.7-14.810.4380.534021217438
6.15-8.70.5110.579046441054
4.76-6.150.5340.589083875979
3.88-4.760.5210.56301283118796
3.28-3.880.4930.525018551741114
2.84-3.280.410.433025182383135
2.5-2.840.2940.308032813125156

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
SBC-Collectdata collection
HKL-2000data reduction
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→33.56 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.846 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.208
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 787 5.1 %RANDOM
Rwork0.198 ---
all0.2 15372 --
obs0.2 15324 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 87 1899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221846
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9582508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3626.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.265154
X-RAY DIFFRACTIONr_chiral_restr0.1070.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021396
X-RAY DIFFRACTIONr_nbd_refined0.2370.2780
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.210
X-RAY DIFFRACTIONr_mcbond_it1.1321.51196
X-RAY DIFFRACTIONr_mcangle_it1.71421850
X-RAY DIFFRACTIONr_scbond_it2.6093747
X-RAY DIFFRACTIONr_scangle_it3.9684.5658
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 55 -
Rwork0.214 1048 -
obs-1103 99.91 %

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