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- PDB-4s12: 1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phospha... -

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Basic information

Entry
Database: PDB / ID: 4s12
Title1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.
ComponentsN-acetylmuramic acid 6-phosphate etherase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / carbon-oxygen lyase activity / peptidoglycan turnover / carbohydrate derivative binding / carbohydrate metabolic process
Similarity search - Function
N-acetylmuramic acid 6-phosphate etherase MurQ / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Helicase, Ruva Protein; domain 3 ...N-acetylmuramic acid 6-phosphate etherase MurQ / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid 6-phosphate etherase
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. palearctica Y11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / 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 / _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

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Assembly

Deposited unit
A: N-acetylmuramic acid 6-phosphate etherase
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,06613
Polymers94,0963
Non-polymers97110
Water17,637979
1
A: N-acetylmuramic acid 6-phosphate etherase
hetero molecules

A: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49910
Polymers62,7302
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9010 Å2
ΔGint-126 kcal/mol
Surface area20700 Å2
MethodPISA
2
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3178
Polymers62,7302
Non-polymers5866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-91 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.287, 81.734, 58.848
Angle α, β, γ (deg.)90.00, 103.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein N-acetylmuramic acid 6-phosphate etherase / / MurNAc-6-P etherase / N-acetylmuramic acid 6-phosphate hydrolase / N-acetylmuramic acid 6-phosphate lyase


Mass: 31365.244 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica Y11 (bacteria)
Strain: DSM 13030 / CIP 106945 / Y11 / Gene: murQ, Y11_42431 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: E7B2C4, UniProt: A0A0H2UKZ5*PLUS, N-acetylmuramic acid 6-phosphate etherase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 7.6 mg/ml, 0.1 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME, Screen: JCSG+ (H7), 0.24M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25%(w/v) PEG 3350, VAPOR DIFFUSION, ...Details: Protein: 7.6 mg/ml, 0.1 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME, Screen: JCSG+ (H7), 0.24M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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, 2014 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 125532 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 15.2
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6249 / Rsym value: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LZJ

4lzj


Resolution: 1.55→29.95 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.406 / SU ML: 0.044
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17002 6306 5 %RANDOM
Rwork0.14333 ---
obs0.14467 119206 99.9 %-
all-119206 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0.37 Å2
2--1.5 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 52 979 7435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197213
X-RAY DIFFRACTIONr_bond_other_d0.0010.027213
X-RAY DIFFRACTIONr_angle_refined_deg1.4782.0059853
X-RAY DIFFRACTIONr_angle_other_deg0.785316605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4055997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30224.043277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.098151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9851569
X-RAY DIFFRACTIONr_chiral_restr0.0860.21183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021490
X-RAY DIFFRACTIONr_mcbond_it1.0541.0823844
X-RAY DIFFRACTIONr_mcbond_other1.0551.0823842
X-RAY DIFFRACTIONr_mcangle_it1.6471.6164889
X-RAY DIFFRACTIONr_mcangle_other1.6471.6164890
X-RAY DIFFRACTIONr_scbond_it1.8411.3743369
X-RAY DIFFRACTIONr_scbond_other1.8411.3743369
X-RAY DIFFRACTIONr_scangle_other2.8461.9664965
X-RAY DIFFRACTIONr_long_range_B_refined6.21510.9479232
X-RAY DIFFRACTIONr_long_range_B_other5.9379.8318688
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 481 -
Rwork0.2 8692 -
obs-8692 99.68 %
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)
113.761-9.26988.076324.2772-10.545515.1140.39710.54170.0521-0.656-0.34250.0713-0.06970.5287-0.05470.0690.0050.00550.02780.0010.0016-13.388213.9-21.5512
20.4278-0.00980.23260.3312-0.07790.3985-0.01070.0419-0.0109-0.0070.0245-0.00990.01680.0468-0.01380.0049-0.00550.0020.0525-0.00190.00420.473217.3448-6.6281
31.92220.324-0.16911.2602-0.55130.9276-0.01440.14580.0393-0.1214-0.0195-0.0287-0.01930.10470.03390.0343-0.01470.01060.09060.00990.00994.191723.9807-19.1872
40.70840.28220.56060.26950.11790.5412-0.02120.153-0.05220.00060.0674-0.0506-0.00790.1039-0.04620.03610.00750.00040.0856-0.02810.070919.809418.11673.1256
50.8311-0.17490.34880.2185-0.11150.72570.0291-0.042-0.0476-0.0175-0.0143-0.002-0.012-0.0561-0.01480.05390.01260.00540.01060.00390.039543.3336-5.318922.9014
61.7421-0.5180.87671.0732-0.70262.1453-0.109-0.2670.07240.21630.0981-0.0122-0.3317-0.22410.01080.09230.0540.00450.0679-0.00640.009231.2872.960830.6296
70.4215-0.16370.39540.28790.03611.02260.02850.0024-0.0947-0.0243-0.014-0.0166-0.0319-0.0649-0.01450.0730.0082-0.00430.0497-0.00280.066139.2622-6.703117.138
82.09920.1039-0.59041.2703-0.79293.96060.09980.15850.0966-0.07490.05770.0779-0.1815-0.0339-0.15760.08150.03870.01280.0698-0.02250.052329.527-6.4856-8.9569
91.60530.37610.74550.48320.0310.88840.08780.0738-0.1426-0.0309-0.0548-0.01930.09140.0626-0.0330.06830.03070.00960.0273-0.01920.065350.9337-12.266812.6506
100.22990.24120.09340.7684-0.24091.3718-0.02760.070.07370.00430.02170.0076-0.19410.02720.00590.06580.0015-0.00620.02940.03020.071157.8029.925712.6303
110.4574-0.05020.0270.4379-0.01950.8214-0.01060.04730.0092-0.0279-0.0425-0.0582-0.08060.08750.05310.04490.00620.00060.02150.0120.050858.9725-1.335318.5614
124.08690.2563-0.30321.8897-0.16662.61770.0248-0.41160.67770.0138-0.074-0.117-0.51080.04110.04930.1091-0.007-0.02390.0508-0.06370.14166.12933.787547.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 120
3X-RAY DIFFRACTION3A121 - 174
4X-RAY DIFFRACTION4A175 - 295
5X-RAY DIFFRACTION5B4 - 101
6X-RAY DIFFRACTION6B102 - 174
7X-RAY DIFFRACTION7B175 - 230
8X-RAY DIFFRACTION8B231 - 295
9X-RAY DIFFRACTION9C8 - 59
10X-RAY DIFFRACTION10C60 - 155
11X-RAY DIFFRACTION11C156 - 232
12X-RAY DIFFRACTION12C233 - 295

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