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- PDB-4n83: X-ray crystal structure of Streptococcus sanguinis dimanganese(II... -

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Basic information

Entry
Database: PDB / ID: 4n83
TitleX-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / OXIDATION-REDUCTION / FLAVIN MONONUCLEOTIDE / MANGANESE
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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
: / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsBoal, A.K. / Rosenzweig, A.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS.
Authors: Makhlynets, O. / Boal, A.K. / Rhodes, D.V. / Kitten, T. / Rosenzweig, A.C. / Stubbe, J.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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_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.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.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.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_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: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
C: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta
E: Ribonucleoside-diphosphate reductase subunit beta
F: Ribonucleoside-diphosphate reductase subunit beta
G: Ribonucleoside-diphosphate reductase subunit beta
H: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,63924
Polymers294,7608
Non-polymers87916
Water1,15364
1
A: Ribonucleoside-diphosphate reductase subunit beta
G: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9106
Polymers73,6902
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-21 kcal/mol
Surface area22320 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase subunit beta
H: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9106
Polymers73,6902
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-20 kcal/mol
Surface area22130 Å2
MethodPISA
3
C: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9106
Polymers73,6902
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-22 kcal/mol
Surface area22220 Å2
MethodPISA
4
E: Ribonucleoside-diphosphate reductase subunit beta
F: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9106
Polymers73,6902
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-19 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.657, 80.224, 166.374
Angle α, β, γ (deg.)90.000, 105.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonucleoside-diphosphate reductase subunit beta


Mass: 36844.977 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: nrdF, SSA_0768 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3CLZ4, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 3000, magnesium formate, pH 7.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.65→29.881 Å / Num. obs: 86753

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N37

3n37


Resolution: 2.65→29.9 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.843 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.622 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 3799 5 %RANDOM
Rwork0.2355 ---
obs0.2377 75270 86.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.28 Å2 / Biso mean: 49.4168 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0.6 Å2
2--1.29 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18625 0 16 64 18705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0219065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217682
X-RAY DIFFRACTIONr_angle_refined_deg0.8061.94925878
X-RAY DIFFRACTIONr_angle_other_deg0.677340786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.59452263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63825.537968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.519153327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2741548
X-RAY DIFFRACTIONr_chiral_restr0.0460.22846
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0221521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024407
LS refinement shellResolution: 2.652→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 92 -
Rwork0.249 1603 -
all-1695 -
obs--26.58 %
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)
10.2071-0.0429-0.36152.2418-0.42861.4140.25730.253-0.1415-0.4525-0.27720.2739-0.2333-0.40580.01990.3620.362-0.22690.5562-0.15380.1856-75.717510.621131.2271
20.30850.0097-0.21180.5263-0.08260.5929-0.02350.0216-0.0778-0.0327-0.08170.02640.08880.03880.10520.1817-0.00140.05390.07560.00160.1281-8.2167-16.993342.2861
30.7276-0.0245-0.23590.58930.26450.6450.03270.0133-0.02080.0007-0.11730.0718-0.0635-0.06460.08450.1387-0.00540.06840.1033-0.05960.124-38.24288.140777.1975
40.8342-0.23980.16150.81290.0120.24130.05420.0301-0.1871-0.1243-0.22110.25820.1133-0.09930.16690.1761-0.07670.07130.1619-0.17370.2873-53.0199-18.428261.9219
51.0261-0.12880.39731.06580.08450.49230.06950.1026-0.05110.1331-0.29660.3467-0.2441-0.18150.22710.37780.1932-0.08970.2349-0.18540.2504-34.919718.9643-1.5492
60.4682-0.21280.20160.87120.31991.19450.02740.0565-0.077-0.005-0.22160.16430.1115-0.06120.19420.18610.02590.00940.1145-0.07990.0928-14.3719-7.8051-6.1427
71.1493-0.83210.5741.95-0.66661.04930.08110.16960.05530.3597-0.25280.3536-0.1989-0.17860.17160.21240.12080.03310.3285-0.20770.2583-78.749527.653260.6037
80.22280.06040.06050.611-0.09220.7746-0.0211-0.03280.0285-0.0272-0.07910.018-0.16970.01980.10020.2086-0.0021-0.00610.0810.00390.0982-7.764817.013339.8014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 287
2X-RAY DIFFRACTION2B3 - 286
3X-RAY DIFFRACTION3C3 - 286
4X-RAY DIFFRACTION4D3 - 286
5X-RAY DIFFRACTION5E3 - 286
6X-RAY DIFFRACTION6F3 - 286
7X-RAY DIFFRACTION7G4 - 286
8X-RAY DIFFRACTION8H4 - 286

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