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- PDB-2e0m: Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) -

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Basic information

Entry
Database: PDB / ID: 2e0m
TitleMutant Human Ribonuclease 1 (T24L, 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: 1.7 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,56421
Polymers29,2752
Non-polymers1,28919
Water7,026390
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,41212
Polymers14,6381
Non-polymers77511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1529
Polymers14,6381
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)61,12942
Polymers58,5504
Non-polymers2,57938
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
crystal symmetry operation3_445-y-1,x-1/2,z+1/41
crystal symmetry operation8_645y+1,-x-1/2,z+1/41
Buried area9760 Å2
ΔGint-300 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.510, 93.510, 94.386
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: 14637.607 Da / Num. of mol.: 2 / Mutation: T24L, 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.: 390 / 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: 3.52 Å3/Da / Density % sol: 65.08 %
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: Apr 23, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 44558 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 34.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 6.3 / % 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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.919 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21364 2242 5 %RANDOM
Rwork0.1943 ---
obs0.19527 42256 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 19 390 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9382786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41623.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6315366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0511516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21029
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1910.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2120.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.51310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32222090
X-RAY DIFFRACTIONr_scbond_it2.0863823
X-RAY DIFFRACTIONr_scangle_it3.1514.5696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 166 -
Rwork0.238 3074 -
obs--99.94 %
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)
16.38050.2288-0.37443.52461.07361.9678-0.08110.2393-0.2857-0.4150.1522-0.46780.05640.1874-0.0711-0.13570.00460.0952-0.2744-0.0379-0.14074.817-61.461-68.459
23.78320.30541.00614.1310.57861.8899-0.17670.08960.1075-0.45030.0050.3902-0.1221-0.13920.1717-0.2015-0.0041-0.0396-0.2721-0.0415-0.2209-11.58-53.717-66.421
36.5516-0.24040.41413.36111.26742.0837-0.072-0.26350.28650.41730.1553-0.4813-0.05140.2024-0.0833-0.1323-0.0035-0.0975-0.2721-0.0385-0.1414.797-78.803-60.754
44.0508-0.4014-1.33294.2050.66612.1102-0.1989-0.1151-0.09590.41550.0170.39620.1334-0.11810.182-0.20620.00510.0324-0.2696-0.0398-0.2235-11.578-86.558-62.796
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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