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- PDB-4d8f: Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - h... -

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Basic information

Entry
Database: PDB / ID: 4d8f
TitleChlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - high Mn)
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / iron / manganese / ribonucleotide reductase / metalloenzyme
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / 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
ACETIC ACID / : / : / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsDassama, L.M.K. / Boal, A.K. / Krebs, C. / Rosenzweig, A.C. / Bollinger Jr., J.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Evidence that the beta subunit of Chlamydia trachomatis ribonucleotide reductase is active with the manganese ion of its manganese(IV)/iron(III) cofactor in site 1.
Authors: Dassama, L.M. / Boal, A.K. / Krebs, C. / Rosenzweig, A.C. / Bollinger, J.M.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,62216
Polymers170,9394
Non-polymers68312
Water9,494527
1
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,93110
Polymers85,4692
Non-polymers4628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-35 kcal/mol
Surface area24990 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6916
Polymers85,4692
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-33 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.221, 97.998, 100.291
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42734.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: CT_828, nrdB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O84835, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHOR STATES THAT THE THE OXIDATION STATES OF THE METAL IONS IN THE STRUCTURE ARE UNKNOWN

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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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 3000, sodium acetate, 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: 1.85, 1.72
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.851
21.721
ReflectionResolution: 2.2→50 Å / Num. obs: 72917

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SYY

1syy


Resolution: 2.2→29.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.872 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3666 5 %RANDOM
Rwork0.1856 ---
obs0.1881 72748 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.25 Å2 / Biso mean: 27.0097 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20.03 Å2
2--0.37 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10802 0 24 527 11353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211057
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.95114951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.79151311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98624.489577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.156151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7951571
X-RAY DIFFRACTIONr_chiral_restr0.0770.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218443
X-RAY DIFFRACTIONr_mcbond_it0.3921.56553
X-RAY DIFFRACTIONr_mcangle_it0.785210603
X-RAY DIFFRACTIONr_scbond_it1.24734504
X-RAY DIFFRACTIONr_scangle_it2.1644.54348
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 259 -
Rwork0.252 4803 -
all-5062 -
obs--94.49 %
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)
10.3982-0.0829-0.08920.03770.02170.3171-0.01240.06630.05440.0192-0.00790.0082-0.0102-0.0180.02030.02880.006-0.00080.02060.00750.04191.395918.7359-15.5067
20.5850.0332-0.22970.0422-0.0140.2592-0.02420.0096-0.0010.03310.0047-0.01430.01540.03050.01950.0320-0.0160.02310.02020.02827.49528.9833-11.6004
30.49390.1022-0.18510.19390.12130.3126-0.06170.02310.0137-0.02430.0276-0.00930.00190.03340.03410.0194-0.0198-0.01090.04390.02630.03428.437925.076732.6933
40.4489-0.1861-0.09350.3619-0.01560.1959-0.02120.0002-0.0069-0.02090.0207-0.00540.0469-0.0510.00050.0297-0.0339-0.01680.0410.02160.01791.516315.556937.2164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 320
2X-RAY DIFFRACTION2B-9 - 324
3X-RAY DIFFRACTION3C-5 - 318
4X-RAY DIFFRACTION4D-1 - 328

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