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- PDB-4p6b: Crystal structure of Est-Y29,a novel penicillin-binding protein/b... -

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Basic information

Entry
Database: PDB / ID: 4p6b
TitleCrystal structure of Est-Y29,a novel penicillin-binding protein/beta-lactamase homolog from a metagenomic library
ComponentsEst-Y29
KeywordsHYDROLASE / Penicillin-Binding Protein / beta-Lactamase / Metagenome
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsNgo, T.D. / Ryu, B.H. / Ju, H.S. / Jang, E.J. / Kim, K.K. / Kim, D.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/ beta-lactamase homologue from a metagenomic library.
Authors: Ngo, T.D. / Ryu, B.H. / Ju, H. / Jang, E.J. / Kim, K.K. / Kim, T.D.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Est-Y29
B: Est-Y29


Theoretical massNumber of molelcules
Total (without water)85,9142
Polymers85,9142
Non-polymers00
Water16,177898
1
A: Est-Y29
B: Est-Y29

A: Est-Y29
B: Est-Y29

A: Est-Y29
B: Est-Y29

A: Est-Y29
B: Est-Y29


Theoretical massNumber of molelcules
Total (without water)343,6568
Polymers343,6568
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area19460 Å2
ΔGint-96 kcal/mol
Surface area106780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.541, 121.541, 155.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Est-Y29


Mass: 42957.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Cell line (production host): XL1-Blue / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 287 K / Method: evaporation
Details: 2.0 M sodium formate, 0.1 M sodium acetate trihydrate buffer (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.00000, 0.97888, 0.97917, 0.96395
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978881
30.979171
40.963951
ReflectionResolution: 1.7→50 Å / Num. obs: 122542 / % possible obs: 99.5 % / Redundancy: 7.2 % / Net I/σ(I): 45

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHENIXrefinement
HKL-2000data scaling
RefinementResolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.376 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18793 6122 5 %RANDOM
Rwork0.17043 ---
obs0.17131 115954 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.102 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 0 898 6836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226089
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.968273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75323.708267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60915967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7461535
X-RAY DIFFRACTIONr_chiral_restr0.0830.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214673
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.641.53821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20826134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98632268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2174.52139
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 453 -
Rwork0.234 8557 -
obs--99.79 %

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