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- PDB-3lyb: Structure of putative endoribonuclease(KP1_3112) from Klebsiella ... -

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Basic information

Entry
Database: PDB / ID: 3lyb
TitleStructure of putative endoribonuclease(KP1_3112) from Klebsiella pneumoniae
ComponentsPutative endoribonuclease
KeywordsHYDROLASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyRutC-like / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.66 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative endoribonuclease(KP1_3112) from Klebsiella pneumoniae
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Putative endoribonuclease
B: Putative endoribonuclease
C: Putative endoribonuclease
D: Putative endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8788
Polymers73,7174
Non-polymers1604
Water50428
1
A: Putative endoribonuclease
B: Putative endoribonuclease
C: Putative endoribonuclease
D: Putative endoribonuclease
hetero molecules

A: Putative endoribonuclease
B: Putative endoribonuclease
C: Putative endoribonuclease
D: Putative endoribonuclease
hetero molecules

A: Putative endoribonuclease
B: Putative endoribonuclease
C: Putative endoribonuclease
D: Putative endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,63324
Polymers221,15212
Non-polymers48112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area32180 Å2
ΔGint-222 kcal/mol
Surface area59620 Å2
MethodPISA
2
C: Putative endoribonuclease

A: Putative endoribonuclease
D: Putative endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3685
Polymers55,2883
Non-polymers802
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation5_555z,x,y1
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-38 kcal/mol
Surface area17780 Å2
MethodPISA
3
B: Putative endoribonuclease
hetero molecules

B: Putative endoribonuclease
hetero molecules

B: Putative endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5299
Polymers55,2883
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5530 Å2
ΔGint-73 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.557, 166.557, 166.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-168-

HOH

21B-169-

HOH

DetailsTrimer or higher assembly(nonamer)

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Components

#1: Protein
Putative endoribonuclease


Mass: 18429.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: NTUH-K2044 / Gene: KP1_3112 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4X9E0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na-Hepes pH 7.5, 28% PEG 400, 02.M CaCl2, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 22307 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.104 / Χ2: 1.276 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.65-2.7210.68710970.968100
2.7-2.7421.10.59110900.984100
2.74-2.821.20.49311211.015100
2.8-2.8521.30.45311051.035100
2.85-2.9221.40.41510901.014100
2.92-2.9821.50.34911131.069100
2.98-3.0621.70.2911261.059100
3.06-3.1421.80.24810781.093100
3.14-3.23220.20111281.09100
3.23-3.34220.1610871.136100
3.34-3.4622.20.12811191.141100
3.46-3.622.30.10811211.256100
3.6-3.7622.20.09510981.295100
3.76-3.96220.0911311.423100
3.96-4.21220.07911141.456100
4.21-4.5321.70.06711161.481100
4.53-4.9821.50.05811211.271100
4.98-5.720.40.06111291.586100
5.7-7.1822.10.0711402.122100
7.18-4020.90.05311831.945100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.66→37.24 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.858 / SU B: 9.55 / SU ML: 0.205 / SU R Cruickshank DPI: 0.543 / SU Rfree: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1123 5.1 %RANDOM
Rwork0.193 ---
obs0.195 22232 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.26 Å2 / Biso mean: 40.752 Å2 / Biso min: 3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.66→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 4 28 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224372
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.965978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75523.246191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44515665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4721532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223360
X-RAY DIFFRACTIONr_mcbond_it0.8071.52711
X-RAY DIFFRACTIONr_mcangle_it1.52224420
X-RAY DIFFRACTIONr_scbond_it1.94231661
X-RAY DIFFRACTIONr_scangle_it3.2984.51558
LS refinement shellResolution: 2.658→2.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 72 -
Rwork0.219 1572 -
all-1644 -
obs--99.58 %

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