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- PDB-3mzr: RNase crystals grown in loops/micromounts -

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Basic information

Entry
Database: PDB / ID: 3mzr
TitleRNase crystals grown in loops/micromounts
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / crystals on loops / RNase from drops
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMathews, I.I.
Citation
Journal: J.Appl.Crystallogr. / Year: 2010
Title: Diffraction study of protein crystals grown in cryoloops and micromounts.
Authors: Berger, M.A. / Decker, J.H. / Mathews, I.I.
#1: Journal: Proteins / Year: 2009
Title: X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability.
Authors: Kurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Imrpoving radiation-damage substructures for RIP.
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.G.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3016
Polymers14,0631
Non-polymers2385
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribonuclease pancreatic
hetero molecules

A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,60112
Polymers28,1252
Non-polymers47610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3170 Å2
ΔGint-79 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 64.190, 63.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 14062.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 295 K / Method: crystals grown in loops / pH: 5.5
Details: 1.7M Ammonium sulfate, 2M NaCal, 0.1M Sodium acetate, pH 5.5, Crystals grown in loops, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 10, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→29 Å / Num. all: 24805 / Num. obs: 24805 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1820

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 3DH5

3dh5


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.238 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19256 1269 5.1 %RANDOM
Rwork0.17628 ---
obs0.17709 23536 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 9 140 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021975
X-RAY DIFFRACTIONr_bond_other_d0.0050.02642
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.931320
X-RAY DIFFRACTIONr_angle_other_deg0.92731576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55425.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38615168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.177154
X-RAY DIFFRACTIONr_chiral_restr0.1020.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1561.5621
X-RAY DIFFRACTIONr_mcbond_other0.3331.5246
X-RAY DIFFRACTIONr_mcangle_it2.05121004
X-RAY DIFFRACTIONr_scbond_it2.9033354
X-RAY DIFFRACTIONr_scangle_it4.6824.5316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 108 -
Rwork0.237 1704 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 25.9223 Å / Origin y: -8.8822 Å / Origin z: -27.5963 Å
111213212223313233
T0.0282 Å2-0.0055 Å2-0.0129 Å2-0.0058 Å2-0.0024 Å2--0.0204 Å2
L0.5035 °20.2121 °20.0184 °2-0.7415 °2-0.1429 °2--0.4813 °2
S-0.0753 Å °0.0089 Å °0.0519 Å °-0.0526 Å °0.0438 Å °0.0149 Å °0.0117 Å °-0.0435 Å °0.0316 Å °

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