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- PDB-5u2g: 2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding P... -

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Basic information

Entry
Database: PDB / ID: 5u2g
Title2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding Protein 1A from Haemophilus influenzae
ComponentsPenicillin-binding protein 1A
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Lipid-Binding Protein
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / response to antibiotic / plasma membrane
Similarity search - Function
Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding Protein 1A from Haemophilus influenzae.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1A
B: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,86429
Polymers186,8102
Non-polymers2,05427
Water5,927329
1
A: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,51415
Polymers93,4051
Non-polymers1,10914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,35114
Polymers93,4051
Non-polymers94613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.448, 111.928, 107.693
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Penicillin-binding protein 1A / PBP1a / Penicillin-binding protein A


Mass: 93405.062 Da / Num. of mol.: 2 / Fragment: residues 32-853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: mrcA, ponA, HI_0440 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic
References: UniProt: P31776, Transferases; Glycosyltransferases; Pentosyltransferases, Hydrolases; Acting on peptide bonds (peptidases)

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Non-polymers , 5 types, 356 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 9.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: Classics II (G5), 0.2M Lithium sulfate, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 62896 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 69.2 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 23.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.792 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.61→29.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.949 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22277 3003 4.8 %RANDOM
Rwork0.17857 ---
obs0.18074 59853 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.22 Å2
2--4.76 Å20 Å2
3----5.25 Å2
Refinement stepCycle: 1 / Resolution: 2.61→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10449 0 102 329 10880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0210758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210092
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.97914541
X-RAY DIFFRACTIONr_angle_other_deg0.9323405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4851336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.22724.055476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.657151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.211576
X-RAY DIFFRACTIONr_chiral_restr0.0870.21598
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02111880
X-RAY DIFFRACTIONr_gen_planes_other0.0190.022188
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_it2.4585.285359
X-RAY DIFFRACTIONr_mcbond_other2.4585.285358
X-RAY DIFFRACTIONr_mcangle_it3.9427.916690
X-RAY DIFFRACTIONr_mcangle_other3.9427.9116691
X-RAY DIFFRACTIONr_scbond_it2.8145.6545399
X-RAY DIFFRACTIONr_scbond_other2.8145.6545399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.438.3417852
X-RAY DIFFRACTIONr_long_range_B_refined6.65161.10211669
X-RAY DIFFRACTIONr_long_range_B_other6.57361.06411635
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 206 -
Rwork0.307 3965 -
obs--89.64 %
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)
12.1292.0898-2.622.1686-2.17195.38270.1544-0.27750.07010.137-0.30430.2075-0.24460.26520.14980.16280.10710.06830.3912-0.01290.275647.656715.4195144.2829
22.27812.3029-2.50623.534-0.81185.33880.29170.63990.84960.01510.13341.2231-0.7688-1.2148-0.42510.14710.18450.10090.72770.08240.655234.251117.148146.7747
32.0739-0.34270.75370.5814-0.19431.3237-0.0361-0.2993-0.06080.06420.12830.1820.0684-0.4118-0.09210.0149-0.00660.01590.32430.11410.122336.443122.9032111.0217
41.0843-0.1141-0.43870.89790.04291.884-0.00950.17060.00650.0060.0389-0.05670.11570.1773-0.02940.0080.0218-0.00390.18110.03420.160764.57219.710692.1196
51.92880.0645-0.02211.3028-0.17671.86960.10840.01210.2049-0.0061-0.055-0.0483-0.0330.0405-0.05340.00940.00250.00330.17030.07390.098358.148928.282493.5013
61.80610.17830.02950.8569-2.04736.18140.00260.02550.04950.0303-0.0537-0.1344-0.4130.30110.05110.1017-0.04280.07390.22030.09120.210574.114936.501779.6738
72.1486-2.19152.91442.5088-2.25665.90220.14420.2387-0.1422-0.1518-0.23810.25090.11010.2210.0940.1864-0.1044-0.0420.4532-0.01670.27544.449756.447817.4197
82.4191-2.4711.64384.1763-0.95364.29740.2854-0.7709-0.9645-0.15350.05681.12640.8694-1.089-0.34220.2251-0.2171-0.09550.71530.08850.6369-8.706855.240214.6173
92.01730.301-0.6560.6733-0.19571.3356-0.04450.24820.0627-0.09040.1290.1822-0.0446-0.3694-0.08450.02080.0022-0.00760.29090.10990.1238-7.148249.210150.3708
101.08970.21840.57270.77980.21232.12930.0287-0.1758-0.0135-0.04110.0273-0.0443-0.11520.2134-0.05590.0158-0.01650.02650.18840.03770.136520.842352.40669.3954
112.03660.3476-0.08611.1601-0.01611.78960.0874-0.1485-0.237-0.0116-0.0409-0.03480.02180.0296-0.04650.01220.00720.01040.18290.08070.096414.476743.791567.9492
121.76960.23450.02780.9298-1.49096.2039-0.0530.036-0.17630.1024-0.0994-0.36710.31040.26980.15240.08830.0332-0.07490.22410.09990.231330.391535.564181.863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 159
2X-RAY DIFFRACTION2A160 - 258
3X-RAY DIFFRACTION3A259 - 449
4X-RAY DIFFRACTION4A450 - 608
5X-RAY DIFFRACTION5A609 - 789
6X-RAY DIFFRACTION6A790 - 831
7X-RAY DIFFRACTION7B40 - 158
8X-RAY DIFFRACTION8B159 - 257
9X-RAY DIFFRACTION9B258 - 449
10X-RAY DIFFRACTION10B450 - 608
11X-RAY DIFFRACTION11B609 - 789
12X-RAY DIFFRACTION12B790 - 831

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