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- PDB-4gyj: Crystal structure of mutant (D318N) bacillus subtilis family 3 gl... -

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Basic information

Entry
Database: PDB / ID: 4gyj
TitleCrystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)
ComponentsUncharacterized lipoprotein ybbD
KeywordsHYDROLASE/substrate / TIM-BARREL / HYDROLASE / HYDROLASE-substrate complex
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / extracellular region / plasma membrane
Similarity search - Function
: / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily ...: / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBacik, J.P. / Mark, B.L.
CitationJournal: Chem.Biol. / Year: 2012
Title: Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.
Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Vocadlo, D.J. / Mark, B.L.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
Revision 1.2Jan 28, 2015Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / refine / refine_hist / software / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.ls_number_reflns_all / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _software.classification / _software.name / _software.version / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized lipoprotein ybbD
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8976
Polymers142,4612
Non-polymers1,4354
Water19,2581069
1
A: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9483
Polymers71,2311
Non-polymers7182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9483
Polymers71,2311
Non-polymers7182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.450, 73.390, 83.430
Angle α, β, γ (deg.)98.65, 110.14, 92.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized lipoprotein ybbD / ORF1


Mass: 71230.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-642 / Mutation: D318N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU01660, NagZ, ybbD, yzbA / Production host: Escherichia coli (E. coli) / References: UniProt: P40406
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 296 K / pH: 7.5
Details: 22% PEG3350, pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9749
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.65→38.61 Å / Num. obs: 147692 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.07 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.742 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
MxDCdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMX

3bmx


Resolution: 1.65→38.61 Å / SU ML: 0.41 / σ(F): 1.97 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 7241 5.06 %
Rwork0.163 --
obs0.164 147676 95.8 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.38 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6931 Å21.589 Å21.3117 Å2
2---3.6265 Å24.1466 Å2
3---0.9334 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9293 0 98 1069 10460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099590
X-RAY DIFFRACTIONf_angle_d1.1513026
X-RAY DIFFRACTIONf_dihedral_angle_d19.6523672
X-RAY DIFFRACTIONf_chiral_restr0.0721523
X-RAY DIFFRACTIONf_plane_restr0.0071696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.34552500.28354618X-RAY DIFFRACTION94
1.6688-1.68840.28452410.26524515X-RAY DIFFRACTION95
1.6884-1.7090.31632360.24864719X-RAY DIFFRACTION94
1.709-1.73060.26632100.2434540X-RAY DIFFRACTION95
1.7306-1.75340.26142320.22934655X-RAY DIFFRACTION95
1.7534-1.77740.26752430.22114624X-RAY DIFFRACTION94
1.7774-1.80280.27312440.21254629X-RAY DIFFRACTION95
1.8028-1.82970.25272290.19634656X-RAY DIFFRACTION94
1.8297-1.85830.22892270.18314620X-RAY DIFFRACTION96
1.8583-1.88880.19862370.17444657X-RAY DIFFRACTION94
1.8888-1.92130.21262490.17534650X-RAY DIFFRACTION96
1.9213-1.95630.23522740.1694614X-RAY DIFFRACTION95
1.9563-1.99390.20642740.174648X-RAY DIFFRACTION96
1.9939-2.03460.2182430.16324639X-RAY DIFFRACTION95
2.0346-2.07880.18552540.16214659X-RAY DIFFRACTION95
2.0788-2.12720.18762610.15944647X-RAY DIFFRACTION96
2.1272-2.18040.22670.15754663X-RAY DIFFRACTION96
2.1804-2.23930.19932630.15824681X-RAY DIFFRACTION96
2.2393-2.30520.19132600.15854686X-RAY DIFFRACTION97
2.3052-2.37960.19522450.15064700X-RAY DIFFRACTION96
2.3796-2.46460.1882520.15214728X-RAY DIFFRACTION96
2.4646-2.56330.18532520.15514680X-RAY DIFFRACTION97
2.5633-2.67990.20472660.1584693X-RAY DIFFRACTION97
2.6799-2.82120.19192690.15974729X-RAY DIFFRACTION97
2.8212-2.99790.18362590.15714729X-RAY DIFFRACTION97
2.9979-3.22920.19692570.1634733X-RAY DIFFRACTION97
3.2292-3.5540.18222580.15894747X-RAY DIFFRACTION98
3.554-4.06780.16172250.14214781X-RAY DIFFRACTION98
4.0678-5.12310.14992630.1334784X-RAY DIFFRACTION98
5.1231-38.61720.15522380.1664774X-RAY DIFFRACTION98
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)
11.2099-0.4125-0.12611.48170.3521.0234-0.05120.0893-0.02-0.03730.0011-0.02010.05610.08190.03270.0613-0.0296-0.02120.05940.00720.052433.9432-38.2055-13.2515
22.0402-0.23790.34972.0456-0.16431.86960.00980.08760.2710.0194-0.04390.1852-0.3098-0.0660.01910.13710.01610.01440.1012-0.01160.151216.6788-7.8473-6.3331
31.07460.1437-0.46871.739-0.16331.5423-0.0044-0.1559-0.01330.1676-0.0085-0.0889-0.06230.1277-0.00350.08510.0231-0.01210.110.02910.060533.8419-16.5626-48.9755
41.567-0.0755-0.55652.0834-0.46851.7244-0.14350.0913-0.2738-0.27030.15310.32960.571-0.27990.00010.3462-0.1016-0.03360.1847-0.00480.188519.5703-48.417-56.4594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 25:428)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 429:642)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 26:428)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 429:642)

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