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- PDB-3jz0: LinB complexed with clindamycin and AMPCPP -

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Basic information

Entry
Database: PDB / ID: 3jz0
TitleLinB complexed with clindamycin and AMPCPP
ComponentsLincosamide nucleotidyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / alpha-beta structure / Transferase / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


transferase activity / identical protein binding / metal ion binding
Similarity search - Function
: / Lincosamide nucleotidyltransferase-like, C-terminal domain / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / CLINDAMYCIN / Lincosamide nucleotidyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorar, M. / Wright, G.D.
CitationJournal: Structure / Year: 2009
Title: Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
Authors: Morar, M. / Bhullar, K. / Hughes, D.W. / Junop, M. / Wright, G.D.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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.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.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: Lincosamide nucleotidyltransferase
B: Lincosamide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78211
Polymers66,8002
Non-polymers1,9829
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-26.6 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.689, 96.064, 102.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Lincosamide nucleotidyltransferase


Mass: 33399.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: linB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9WVY4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CLY / CLINDAMYCIN


Mass: 424.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H33ClN2O5S / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 20% PEG 3350, 0.1M Magnesium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42525 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.096 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2073 / Rsym value: 0.368 / % possible all: 94.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JYY

3jyy


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.512 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22052 2130 5 %RANDOM
Rwork0.1687 ---
all0.17132 40327 --
obs0.17132 40327 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---1.42 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 121 716 5183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224622
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9996274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3755556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44725.268224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3091519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023395
X-RAY DIFFRACTIONr_mcbond_it0.3771.52688
X-RAY DIFFRACTIONr_mcangle_it0.75324346
X-RAY DIFFRACTIONr_scbond_it1.37531934
X-RAY DIFFRACTIONr_scangle_it2.2284.51916
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1789 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.722
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 154 -
Rwork0.213 2852 -
obs--94.71 %
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)
10.2540.1211-0.0440.3745-0.05470.01560.0032-0.00070.0002-0.0094-0.0079-0.03210.0052-0.00410.00470.01440.00340.00110.0133-0.00130.00367.087414.382621.6996
20.2624-0.09540.15620.4118-0.00920.13950.05140.0118-0.0288-0.0434-0.0302-0.04240.02440.0168-0.02120.01240.0048-0.00150.01030.00480.01140.2508-3.935716.1201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 267
2X-RAY DIFFRACTION1A300 - 900
3X-RAY DIFFRACTION1A268 - 2353
4X-RAY DIFFRACTION2B2 - 267
5X-RAY DIFFRACTION2B301 - 900
6X-RAY DIFFRACTION2B268 - 2322

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