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- PDB-2rcc: Crystal structure of putative class I ribonucleotide reductase (N... -

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Basic information

Entry
Database: PDB / ID: 2rcc
TitleCrystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / NP_241368.1 / Putative Class I Ribonucleotide Reductase / Ribonucleotide reductase / small chain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA replication / Iron / Metal-binding
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
C: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,14719
Polymers122,5663
Non-polymers1,58116
Water6,125340
1
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,75012
Polymers81,7112
Non-polymers1,04010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules

C: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,79314
Polymers81,7112
Non-polymers1,08312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,y,-z1
Buried area4970 Å2
MethodPISA
3
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
C: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
C: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,29438
Polymers245,1326
Non-polymers3,16232
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,y,-z1
Buried area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.260, 72.780, 111.770
Angle α, β, γ (deg.)90.000, 124.900, 90.000
Int Tables number5
Space group name H-MC121
DetailsTHE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit


Mass: 40855.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: NP_241368.1, nrdB, BH0502 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9KFH7, ribonucleoside-diphosphate reductase

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Non-polymers , 7 types, 356 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 10.0% Glycerol, 5.0% PEG 3000, 30.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
ReflectionResolution: 1.9→28.502 Å / Num. obs: 90521 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.44 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.3891.72143217841197
1.97-2.050.2992.32135317649198.3
2.05-2.140.21932073316951198.3
2.14-2.250.16542104317259198.6
2.25-2.390.12752149817591198.8
2.39-2.580.0976.42240518280198.9
2.58-2.840.078.32160917685198.9
2.84-3.250.05410.72156317636198.8
3.25-4.080.041142091017470198.7
4.08-28.5020.032162135417437196

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.502 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.078 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ZINC HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITES OF MOLECULES B AND C BASED ON A X-RAY FLUORESCENCE SCAN FOR METAL, PRESENCE OF ELECTRON DENSITY AND COORDINATION GEOMETRY. 5. ETHYLENE GLYCOL, GLYCEROL, AND PARTIAL PEG MOLECULES HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6. THERE IS A LARGE BLOB OF UNIDENTIFIED DENSITY IN THE VICINITY OF AMINO ACIDS A25-A28.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4538 5 %RANDOM
Rwork0.183 ---
obs0.184 90520 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.585 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-0.95 Å2
2---0.46 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 80 340 7748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227762
X-RAY DIFFRACTIONr_bond_other_d0.0040.025146
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.94710567
X-RAY DIFFRACTIONr_angle_other_deg1.292312592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6355954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80124.84374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.015151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021523
X-RAY DIFFRACTIONr_chiral_restr0.0920.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021623
X-RAY DIFFRACTIONr_nbd_refined0.1940.31811
X-RAY DIFFRACTIONr_nbd_other0.1410.35067
X-RAY DIFFRACTIONr_nbtor_refined0.1830.53861
X-RAY DIFFRACTIONr_nbtor_other0.0880.53452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5561
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.377
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.523
X-RAY DIFFRACTIONr_mcbond_it2.15835257
X-RAY DIFFRACTIONr_mcbond_other0.57831825
X-RAY DIFFRACTIONr_mcangle_it2.93257533
X-RAY DIFFRACTIONr_scbond_it5.53783551
X-RAY DIFFRACTIONr_scangle_it7.089113009
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 310 -
Rwork0.255 6275 -
all-6585 -
obs--98.74 %
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)
10.4695-0.04860.05481.64560.31770.5170.04450.0328-0.0623-0.0043-0.0648-0.0606-0.0538-0.04450.02030.04930.0253-0.02550.05370.00110.0424-143.3624-55.295931.1436
229.322720.73226.605514.65844.67031.4881.1325-1.5321-1.11080.7873-1.5866-0.4904-0.8034-1.50270.4540.4789-0.0248-0.13970.489-0.09310.31-142.712-54.504246.1934
31.18110.86460.66971.46750.68030.64570.04380.023-0.08090.1333-0.0247-0.15390.0165-0.021-0.01910.09540.0081-0.02770.0650.00470.1254-137.7368-53.176940.769
42.32322.09480.37512.07690.29190.08350.2192-0.36230.36370.2308-0.27060.2767-0.0396-0.15760.05140.0882-0.01570.05390.1172-0.08210.1393-152.8047-50.50243.5788
51.2110.71970.44391.97160.43460.7407-0.0263-0.08950.1999-0.1034-0.150.2856-0.1569-0.16810.17620.07960.0486-0.0390.0402-0.05080.118-150.022-39.969535.306
61.24550.10081.00392.23540.89123.5895-0.00320.13840.1074-0.157-0.0303-0.2539-0.18770.2390.03350.0270.00730.02070.06350.0120.0809-131.6645-67.677819.648
71.0711-0.24160.3691.41190.01830.84720.03380.0278-0.0834-0.0786-0.07450.04160.0253-0.01350.04060.0820.021-0.02290.0436-0.0160.0871-140.9911-76.810725.1538
80.6974-0.25880.15632.256-0.22711.16620.0298-0.0947-0.06020.2056-0.0617-0.19020.07920.07220.03190.0640.0202-0.01750.06360.00520.0834-133.4306-82.222434.6733
91.11-0.15450.54521.3945-0.44353.41820.0520.0999-0.1367-0.1567-0.1187-0.1350.09590.27080.06670.09540.05940.02260.0428-0.02650.1189-129.1769-89.049123.977
102.9793-0.5999-0.5821.3668-2.47096.10710.08190.1173-0.08030.0649-0.1332-0.21360.30290.57310.05140.02360.04950.03660.0878-0.04180.1087-122.9436-89.028526.0261
111.8102-0.25150.02730.11830.23671.0789-0.0678-0.19430.0365-0.01210.0804-0.1026-0.1005-0.0442-0.01260.09390.02070.01370.1373-0.01670.0089-177.9773-63.71496.6712
121.6698-0.27371.08861.07570.59521.2904-0.29230.07940.0218-0.430.2568-0.0075-0.1002-0.04290.03550.1708-0.04270.03510.22440.01330.0902-185.0745-61.15522.8251
136.14791.9743-0.23621.6848-0.83442.0855-0.1720.52830.8251-0.17060.10050.3466-0.1444-0.38370.07150.11970.08220.05980.23230.0490.064-187.1969-51.757712.469
142.47731.0060.9022.21240.73970.40570.02230.066-0.10990.18070.1292-0.01620.1234-0.0301-0.15150.1053-0.04740.03850.2310.02340.0047-186.1047-70.220913.9083
153.56891.10820.68342.12941.10261.97460.094-0.32950.05370.2344-0.0234-0.0128-0.082-0.1034-0.07070.0680.02460.07870.1303-0.0162-0.0346-187.7645-58.248525.0528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 842 - 85
2X-RAY DIFFRACTION2AA85 - 9586 - 96
3X-RAY DIFFRACTION3AA96 - 14897 - 149
4X-RAY DIFFRACTION4AA149 - 193150 - 194
5X-RAY DIFFRACTION5AA194 - 312195 - 313
6X-RAY DIFFRACTION6BB37 - 7138 - 72
7X-RAY DIFFRACTION7BB72 - 21073 - 211
8X-RAY DIFFRACTION8BB211 - 266212 - 267
9X-RAY DIFFRACTION9BB267 - 297268 - 298
10X-RAY DIFFRACTION10BB298 - 315299 - 316
11X-RAY DIFFRACTION11CC3 - 874 - 88
12X-RAY DIFFRACTION12CC88 - 14489 - 145
13X-RAY DIFFRACTION13CC145 - 193146 - 194
14X-RAY DIFFRACTION14CC194 - 230195 - 231
15X-RAY DIFFRACTION15CC231 - 312232 - 313

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