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- PDB-2e0l: Mutant Human Ribonuclease 1 (Q28L, R31L, R32L) -

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Basic information

Entry
Database: PDB / ID: 2e0l
TitleMutant Human Ribonuclease 1 (Q28L, R31L, R32L)
ComponentsRibonuclease
KeywordsHYDROLASE / Mutant Human Pancreatic Ribonuclease 1
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYamada, H. / Tamada, T. / Kosaka, M. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2007
Title: 'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with ...Title: 'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines
Authors: Yamada, H. / Tamada, T. / Kosaka, M. / Miyata, K. / Fujiki, S. / Tano, M. / Moriya, M. / Yamanishi, M. / Honjo, E. / Tada, H. / Ino, T. / Yamaguchi, H. / Futami, J. / Seno, M. / Nomoto, T. / ...Authors: Yamada, H. / Tamada, T. / Kosaka, M. / Miyata, K. / Fujiki, S. / Tano, M. / Moriya, M. / Yamanishi, M. / Honjo, E. / Tada, H. / Ino, T. / Yamaguchi, H. / Futami, J. / Seno, M. / Nomoto, T. / Hirata, T. / Yoshimura, M. / Kuroki, R.
History
DepositionOct 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,54021
Polymers29,2512
Non-polymers1,28919
Water6,882382
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,40012
Polymers14,6261
Non-polymers77511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1409
Polymers14,6261
Non-polymers5148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Ribonuclease
hetero molecules

A: Ribonuclease
hetero molecules

B: Ribonuclease
hetero molecules

B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,08142
Polymers58,5024
Non-polymers2,57938
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_465-x-1,-y+1,z1
crystal symmetry operation4_354y-3/2,-x,z-1/41
crystal symmetry operation7_564-y+1/2,x+1,z-1/41
Buried area9650 Å2
ΔGint-303 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.376, 93.376, 93.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1001-

CD

DetailsThe biological assembly is a monomer

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Components

#1: Protein Ribonuclease / Ribonuclease 1 / RNase 1 / RNase A / RNase UpI-1 / RIB-1 / HP-RNase


Mass: 14625.553 Da / Num. of mol.: 2 / Mutation: Q28L, R31L, R32L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBO26 / Production host: Escherichia coli (E. coli) / References: UniProt: P07998, EC: 3.1.27.5
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 30% PEG 400, 0.1M cadmium chloride, 0.1M sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 52471 / % possible obs: 99.7 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7RSA

7rsa


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.571 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21496 2663 5.1 %RANDOM
Rwork0.19422 ---
obs0.19528 49597 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.495 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 19 382 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9342784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01723.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73615364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5491516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2968
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2350.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2150.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.51312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.322092
X-RAY DIFFRACTIONr_scbond_it2.213818
X-RAY DIFFRACTIONr_scangle_it3.4064.5692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 206 -
Rwork0.261 3649 -
obs--99.48 %
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)
15.989-0.21230.44023.39431.32682.1805-0.1186-0.22820.29710.35110.1825-0.4951-0.03750.1884-0.0639-0.15030.0034-0.0881-0.2586-0.0449-0.0773-41.73661.17961.884
24.2688-0.4675-1.13514.25230.50531.7336-0.189-0.1637-0.0780.38040.01750.39250.1035-0.130.1715-0.2090.01310.0298-0.2533-0.0347-0.154-58.25153.69260.09
36.14080.2644-0.40013.49841.26362.1012-0.15580.2446-0.3152-0.37320.1985-0.50630.050.206-0.0427-0.1464-0.00750.0969-0.2545-0.0469-0.079-41.7178.91554.355
44.29820.57581.08014.27660.66851.3913-0.21050.17650.0769-0.4060.03210.363-0.0947-0.13520.1784-0.2013-0.0151-0.0285-0.2559-0.0339-0.1549-58.24786.41756.119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 482 - 49
2X-RAY DIFFRACTION1AA80 - 10281 - 103
3X-RAY DIFFRACTION2AA49 - 7950 - 80
4X-RAY DIFFRACTION2AA103 - 128104 - 129
5X-RAY DIFFRACTION3BB1 - 482 - 49
6X-RAY DIFFRACTION3BB80 - 10281 - 103
7X-RAY DIFFRACTION4BB49 - 7950 - 80
8X-RAY DIFFRACTION4BB103 - 128104 - 129

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