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Entry
Database: PDB / ID: 5uh0
Title1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.
ComponentsMembrane-bound lytic murein transglycosylase F
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Membrane-bound Lytic Murein Transglycosylase F
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process
Similarity search - Function
Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Shuvalova, L. / Flores, K. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.
Authors: Minasov, G. / Shuvalova, L. / Flores, K. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase F
B: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9334
Polymers54,8622
Non-polymers712
Water3,567198
1
A: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4672
Polymers27,4311
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4672
Polymers27,4311
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Membrane-bound lytic murein transglycosylase F
hetero molecules

B: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9334
Polymers54,8622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area2120 Å2
ΔGint-29 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.086, 66.507, 96.427
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 33 - 265 / Label seq-ID: 2 - 234

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Membrane-bound lytic murein transglycosylase F / Murein lyase F


Mass: 27431.184 Da / Num. of mol.: 2 / Fragment: UNP residues 35-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mltF, YPO2922, y1308, YP_2535 / Plasmid: pMCSG53
Production host: Escherichia coli BL21(DE3) magic (bacteria)
Strain (production host): BL21 (DE3) magic
References: UniProt: Q74SQ6, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 17.3 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1 Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 30781 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rsym value: 0.11 / Net I/σ(I): 29.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1503 / CC1/2: 0.895 / Rpim(I) all: 0.277 / Rsym value: 0.7 / Χ2: 0.995 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OWD

4owd


Resolution: 1.95→29.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.225 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26735 1513 4.9 %RANDOM
Rwork0.21327 ---
obs0.216 29200 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.574 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---2.23 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 2 198 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193909
X-RAY DIFFRACTIONr_bond_other_d0.0010.023583
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.985323
X-RAY DIFFRACTIONr_angle_other_deg0.8738341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4465497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4924.468188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5815661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4931526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.024460
X-RAY DIFFRACTIONr_gen_planes_other0.020.02798
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_it2.4492.2641940
X-RAY DIFFRACTIONr_mcbond_other2.4432.2631939
X-RAY DIFFRACTIONr_mcangle_it3.5283.3742453
X-RAY DIFFRACTIONr_mcangle_other3.5293.3762454
X-RAY DIFFRACTIONr_scbond_it3.3912.6931969
X-RAY DIFFRACTIONr_scbond_other3.392.6951970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1143.8992871
X-RAY DIFFRACTIONr_long_range_B_refined6.95228.0354457
X-RAY DIFFRACTIONr_long_range_B_other6.89427.8154414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15010 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 102 -
Rwork0.256 2131 -
obs--99.55 %
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)
11.2539-0.2743-0.49023.0781-0.02051.33740.05480.0524-0.00260.2651-0.02710.2887-0.0243-0.1536-0.02770.0293-0.00230.02450.0334-0.00920.04232.0162.608427.6942
21.4075-0.4671.49721.4641-1.02793.70480.12650.2399-0.0801-0.3319-0.0721-0.0440.17810.2732-0.05440.09050.02420.02850.0585-0.00960.043231.74966.94959.4535
31.62450.2688-0.45841.99461.18693.705-0.130.25090.0192-0.3690.1213-0.0966-0.3583-0.0410.00870.17260.01490.01320.0680.00260.048929.481317.5195.876
43.45541.7949-1.63943.4054-1.48795.0438-0.0892-0.030.0105-0.37350.03660.22920.4687-0.14970.05260.15230.0242-0.03610.078-0.02680.033923.08326.13275.498
51.9363-0.2024-1.00521.9545-0.03390.68880.01610.2028-0.108-0.1099-0.1305-0.00860.1055-0.1640.11440.1078-0.01450.0080.1003-0.02510.089440.5069-3.427122.9749
61.6594-0.05720.49634.0163-0.08991.34290.0283-0.00520.0446-0.4082-0.03530.4162-0.0344-0.16040.0070.05150.005-0.0390.0754-0.00110.04631.9313-1.5924-30.3937
71.02260.1026-0.76882.3274-0.26372.19340.0638-0.10540.01090.1226-0.10320.0038-0.01290.03520.03940.0328-0.0418-0.02490.07550.01080.060433.5322-11.8517-16.6259
81.91890.70721.0462.34460.29955.5099-0.0245-0.1989-0.11590.2857-0.0009-0.06140.1720.07340.02540.1101-0.02130.00360.05890.01590.024129.9259-21.4672-5.1111
90.2928-0.0096-0.02171.21970.20641.44930.0598-0.0715-0.04150.1982-0.12480.1362-0.1519-0.12740.06490.074-0.02050.00070.0741-0.01510.034528.5703-8.7617-12.0815
102.58010.7953-1.79551.67-0.62274.7435-0.0273-0.23450.12550.3595-0.1972-0.1918-0.25-0.32630.22450.17160.0451-0.03690.1873-0.04210.130539.61186.857-20.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 116
2X-RAY DIFFRACTION2A117 - 140
3X-RAY DIFFRACTION3A141 - 187
4X-RAY DIFFRACTION4A188 - 224
5X-RAY DIFFRACTION5A225 - 265
6X-RAY DIFFRACTION6B33 - 87
7X-RAY DIFFRACTION7B88 - 141
8X-RAY DIFFRACTION8B142 - 182
9X-RAY DIFFRACTION9B183 - 241
10X-RAY DIFFRACTION10B242 - 265

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