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- PDB-4m1h: X-ray crystal structure of Chlamydia trachomatis apo NrdB -

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Basic information

Entry
Database: PDB / ID: 4m1h
TitleX-ray crystal structure of Chlamydia trachomatis apo NrdB
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / ribonucleotide reductase
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, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsBoal, A.K. / Rosenzweig, A.C.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Basis for Assembly of the Mn(IV)/Fe(III) Cofactor in the Class Ic Ribonucleotide Reductase from Chlamydia trachomatis.
Authors: Dassama, L.M. / Krebs, C. / Bollinger, J.M. / Rosenzweig, A.C. / Boal, A.K.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)170,9394
Polymers170,9394
Non-polymers00
Water15,997888
1
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta


Theoretical massNumber of molelcules
Total (without water)85,4692
Polymers85,4692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-36 kcal/mol
Surface area25600 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta


Theoretical massNumber of molelcules
Total (without water)85,4692
Polymers85,4692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-36 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.975, 97.394, 99.237
Angle α, β, γ (deg.)90.000, 97.760, 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 / Production host: Escherichia coli (E. coli)
References: UniProt: O84835, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium acetate, 10% PEG3000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.078
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2012 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.695→29.748 Å / Num. all: 156375 / Num. obs: 155357 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rsym value: 0.063 / Net I/σ(I): 28.6
Reflection shellHighest resolution: 1.695 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYY

1syy


Resolution: 1.695→29.748 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.635 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 7791 5 %RANDOM
Rwork0.1794 ---
obs0.1809 155357 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.63 Å2 / Biso mean: 27.509 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20.18 Å2
2--1.22 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.695→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10946 0 0 888 11834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211189
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.95115131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.63751328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66424.564585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.838152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1061571
X-RAY DIFFRACTIONr_chiral_restr0.0770.21639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218527
X-RAY DIFFRACTIONr_mcbond_it0.481.56626
X-RAY DIFFRACTIONr_mcangle_it0.962210737
X-RAY DIFFRACTIONr_scbond_it1.63334563
X-RAY DIFFRACTIONr_scangle_it2.794.54394
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 549 -
Rwork0.287 10316 -
all-10865 -
obs--93.74 %
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)
10.5851-0.0066-0.04540.03440.02960.1887-0.0425-0.05180.0173-0.03550.01370.00590.0032-0.02980.02880.0532-0.006-0.00280.0402-0.02490.0617-20.670816.4897-37.5691
20.56920.1192-0.04970.0607-0.08930.2732-0.052-0.090.0902-0.02620.0024-0.0073-0.00220.00720.04960.0441-0.00640.00250.0463-0.02450.05475.301526.5278-33.4601
30.3890.1301-0.10780.34150.10720.2144-0.01390.0184-0.00430.04430.01990.03730.06810.0959-0.00590.04690.03150.00010.0811-0.02540.027-8.252222.911912.6015
40.4985-0.1533-0.25320.11660.02080.4452-0.0571-0.0030.05050.016-0.00350.02990.0441-0.01910.06060.02080.0028-0.00060.0444-0.03720.1005-35.555432.819217.5239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 322
2X-RAY DIFFRACTION2B-7 - 328
3X-RAY DIFFRACTION3C-1 - 329
4X-RAY DIFFRACTION4D-5 - 328

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