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- PDB-4kd4: Crystal structure of Staphylococcal nuclease variant V23L/L25V/V6... -

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Basic information

Entry
Database: PDB / ID: 4kd4
TitleCrystal structure of Staphylococcal nuclease variant V23L/L25V/V66I/I72V at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / pdtp / cavity / pressure
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsCaro, J.A. / Flores, E. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B.
CitationJournal: To be Published
Title: Pressure effects in proteins
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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_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_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: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4995
Polymers16,8431
Non-polymers6554
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.640, 47.640, 62.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16843.330 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23L,L25V,V66I,I72V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2011
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 20413 / Num. obs: 20413 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.034 / Χ2: 1.327 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.55-1.58100.19513.810051.00399.6
1.58-1.6110.60.15610291.02299.9
1.61-1.6411.30.13810181.03499.7
1.64-1.6712.70.1269881.07299.7
1.67-1.7112.70.10710251.06299.8
1.71-1.7512.30.08810201.13799.9
1.75-1.7913.40.07610121.187100
1.79-1.8413.20.06510241.16799.9
1.84-1.8912.60.05610001.23799.9
1.89-1.9513.10.04510111.237100
1.95-2.0213.10.0410331.23199.9
2.02-2.112.80.03510161.263100
2.1-2.213.50.03110181.265100
2.2-2.3212.70.0310301.402100
2.32-2.4613.20.02810061.412100
2.46-2.6512.80.02510391.391100
2.65-2.9213.30.02510121.476100
2.92-3.3412.90.02310281.47999.9
3.34-4.21130.0310401.724100
4.21-5012.40.04210592.52999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.96 Å
Translation2.5 Å37.96 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNC

1snc


Resolution: 1.55→47.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2388 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8691 / SU B: 2.754 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0826 / SU Rfree: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1045 5.1 %RANDOM
Rwork0.1766 ---
all0.1786 20389 --
obs0.1786 20389 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.28 Å2 / Biso mean: 27.8364 Å2 / Biso min: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 39 96 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.9962.0171624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53724.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.884155
X-RAY DIFFRACTIONr_chiral_restr0.1440.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021854
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 73 -
Rwork0.254 1389 -
all-1462 -
obs-1462 99.73 %
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)
13.2377-0.5857-0.4863.5153-0.73863.19720.26070.0336-0.1676-0.1564-0.1267-0.20990.07150.2448-0.13410.1427-0.0085-0.02330.16780.00230.0817-9.9508-3.20690.2608
23.4050.3099-2.56680.6819-0.83954.37920.5848-0.13250.41710.0534-0.046-0.0075-0.9520.0527-0.53880.3018-0.02190.10450.10210.00380.1172-16.14639.10943.9462
31.8225-0.0249-0.42531.3646-0.12214.08820.0502-0.0717-0.0999-0.04410.0291-0.0012-0.04990.0899-0.07930.1029-0.0144-0.03170.13870.01840.0893-15.5406-3.34211.2166
41.7215-0.4548-1.131.2920.80876.26420.24340.1601-0.0339-0.0498-0.07230.2124-0.6137-0.9357-0.17110.11790.08410.01720.25260.05530.0623-28.30173.51825.8652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 30
2X-RAY DIFFRACTION2A31 - 62
3X-RAY DIFFRACTION3A63 - 97
4X-RAY DIFFRACTION4A98 - 141

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