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- PDB-3h8u: Crystal structure of uncharacterized conserved protein with doubl... -

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Basic information

Entry
Database: PDB / ID: 3h8u
TitleCrystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
Componentsuncharacterized conserved protein with double-stranded beta-helix domain
Keywordsstructural genomics / unknown function / YP_001338853.1 / uncharacterized conserved protein with double-stranded beta-helix domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Cupin domain
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized conserved protein with double-stranded beta-helix domain
B: uncharacterized conserved protein with double-stranded beta-helix domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6166
Polymers26,9172
Non-polymers6994
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-41 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.850, 46.850, 94.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein uncharacterized conserved protein with double-stranded beta-helix domain


Mass: 13458.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: KPN78578_51600, KPN_pKPN5p08243, YP_001338853.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TJ50
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.7000M (NH4)2SO4, 15.0000% Glycerol, 1.7000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97965
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979651
ReflectionResolution: 1.8→24.953 Å / Num. obs: 21525 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.86 % / Biso Wilson estimate: 19.864 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.4911.4455313759192.7
1.86-1.940.36265674438195.8
1.94-2.030.2342.962854251196.4
2.03-2.130.183.757223870196.3
2.13-2.270.1334.964644374196.6
2.27-2.440.1045.860194088196.9
2.44-2.690.0827.363264295197.7
2.69-3.070.05510.361184146198
3.07-3.870.0414.562734258197.7
3.87-24.9530.03317.363264311198.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→24.953 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.999 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A SULPHATE CATION, GLYCEROL AND PEG FRAGMNET (2PE) MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1044 4.9 %RANDOM
Rwork0.152 ---
obs0.154 21489 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.98 Å2 / Biso mean: 31.881 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å20 Å2
2--0.41 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 27 207 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211925
X-RAY DIFFRACTIONr_bond_other_d0.0020.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9242645
X-RAY DIFFRACTIONr_angle_other_deg0.77433934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57124.53586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93915271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.859157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022223
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02372
X-RAY DIFFRACTIONr_nbd_refined0.1990.2308
X-RAY DIFFRACTIONr_nbd_other0.1810.21706
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2871
X-RAY DIFFRACTIONr_nbtor_other0.0820.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.215
X-RAY DIFFRACTIONr_mcbond_it0.7561.51238
X-RAY DIFFRACTIONr_mcbond_other0.2141.5501
X-RAY DIFFRACTIONr_mcangle_it1.21421986
X-RAY DIFFRACTIONr_scbond_it1.9953753
X-RAY DIFFRACTIONr_scangle_it3.2134.5650
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 56 -
Rwork0.217 1480 -
all-1536 -
obs--98.34 %
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)
112.7646-4.39060.62055.05780.56622.3682-0.2143-0.6326-0.29850.14640.05690.30940.2845-0.09940.1574-0.1357-0.0349-0.023-0.1180.0465-0.201416.19917.54227.309
22.2028-0.2034-0.350.61390.33071.9851-0.0076-0.0044-0.0979-0.0718-0.006-0.08930.00250.13130.0136-0.2008-0.00190.0006-0.18570.0133-0.208722.61519.47110.932
312.9662-6.1159-5.88575.32083.17165.44560.56070.01410.684-0.6237-0.14070.0772-1.147-0.4798-0.420.080.07020.02060.00290.0149-0.076111.05136.3559.754
41.2823-0.4971-0.71811.34510.60552.29880.0635-0.07390.098-0.0101-0.07960.0488-0.1927-0.08940.0162-0.1939-0.0176-0.0008-0.1472-0.0053-0.19884.82828.65519.296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 30
2X-RAY DIFFRACTION2A31 - 124
3X-RAY DIFFRACTION3B11 - 29
4X-RAY DIFFRACTION4B30 - 124

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