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- PDB-3rxz: Crystal structure of putative polysaccharide deacetylase from Myc... -

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Basic information

Entry
Database: PDB / ID: 3rxz
TitleCrystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis
ComponentsPolysaccharide deacetylase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / carbohydrate esterase family 4
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Peptidoglycan deacetylase PgdA-like / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Polysaccharide deacetylase, putative
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsMichalska, K. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis
Authors: Michalska, K. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Polysaccharide deacetylase
B: Polysaccharide deacetylase
C: Polysaccharide deacetylase
D: Polysaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,06412
Polymers133,6614
Non-polymers4038
Water6,593366
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-281 kcal/mol
Surface area36470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.212, 59.592, 130.387
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polysaccharide deacetylase


Mass: 33415.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_4373 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: A0R0G0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M NaCl, 0.1 M imidazole/HCl, 30% PEG8K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 14, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 81570 / Num. obs: 81277 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 31.34 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.7
Reflection shellResolution: 2.01→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
SHELXDphasing
SHELXEmodel building
RESOLVEmodel building
DMmodel building
ARP/wARPmodel building
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→29.13 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9243 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1216 1.5 %thin resolution shells
Rwork0.175 ---
all0.1756 81256 --
obs0.1756 81256 --
Displacement parametersBiso mean: 39.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.6123 Å20 Å25.145 Å2
2---13.554 Å20 Å2
3---7.9417 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.01→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 8 366 9290
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0149220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1212609HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4048SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes197HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1369HARMONIC5
X-RAY DIFFRACTIONt_it9220HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion2.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1176SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11198SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2562 64 1.16 %
Rwork0.2255 5443 -
all0.2258 5507 -
obs-5507 -
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)
13.07-0.9309-1.50890.79531.02241.564-0.11480.11180.14550.0240.02370.0251-0.20050.14690.0911-0.05640.0173-0.0370.0773-0.0018-0.0836-10.770310.1788103.8572
22.0469-0.01010.54660.96420.07121.2879-0.0603-0.52440.29080.0322-0.01070.0412-0.24690.13440.071-0.04450.0351-0.04140.1059-0.0723-0.0939-11.722812.342114.776
32.809-0.3893-0.0350.56550.6243.1123-0.1565-0.06150.5058-0.15240.16-0.0755-0.55880.4836-0.00350.031-0.0669-0.0615-0.0916-0.02320.0316-5.855120.352599.7831
40.54810.00410.0050-0.29442.4173-0.044-0.07350.044-0.09610.0197-0.0153-0.0674-0.37450.0243-0.03350.0307-0.04860.056-0.056-0.01-18.8737-0.073102.8764
51.45780.02020.31070.6176-0.01391.3656-0.0915-0.05970.0567-0.05790.0493-0.0503-0.00570.37980.0422-0.05750.016-0.00760.0593-0.0221-0.07-3.76234.0933101.6008
62.1403-0.33841.31930.862-0.42150.8094-0.0191-0.23440.08060.0247-0.1149-0.0214-0.0469-0.01820.134-0.11370.04210.00730.21960.0123-0.1307-36.23990.4315119.59
70.54710.28150.46290.43310.30360.6101-0.0003-0.5020.0059-0.0115-0.03830.09550.0269-0.47650.0386-0.18280.05680.0180.2858-0.0187-0.1711-47.5645-0.9117120.8686
81.98790.725-0.09230.7389-0.70981.3021-0.0226-0.52640.21950.16-0.20210.0455-0.2681-0.18910.2246-0.10320.1181-0.02620.2669-0.133-0.1596-33.3478.7381125.7405
9-0.0209-0.75850.10040.8648-0.39180.2615-0.0260.0150.0591-0.15590.04270.0395-0.0099-0.0038-0.0167-0.09760.0128-0.01450.24020.0391-0.1194-35.9487-4.4485104.2895
101.76050.06950.47080.89870.29061.2880.0584-0.5132-0.12110.0382-0.0334-0.07540.0524-0.2146-0.025-0.11160.02690.00340.19610.0546-0.1313-29.5333-5.2912122.501
111.78120.2070.18110.3323-0.19411.8012-0.00730.386-0.41610.06770.07610.02030.2677-0.2726-0.0687-0.0643-0.02050.01870.0025-0.0679-0.0289-46.5305-15.458384.5572
121.9368-0.0648-0.2630.39620.53561.20450.01180.44620.0076-0.0895-0.01140.06390.0131-0.329-0.0004-0.08760.0016-0.02110.1677-0.0224-0.0758-58.6801-7.321884.232
130.7083-0.1519-0.71510.69960.08170.1718-0.0271-0.0584-0.18040.0141-0.0280.12970.0295-0.36410.0551-0.0672-0.0271-0.00080.1537-0.0238-0.0226-59.7169-10.52797.6193
142.5299-0.13430.5110.40230.30350.0752-0.00920.04970.0028-0.0089-0.00620.05320.01760.01580.0155-0.0447-0.0473-0.02930.0959-0.0021-0.0833-38.695-9.208993.2055
152.2279-0.24350.11770.66160.05160.9721-0.0212-0.2238-0.50660.04610.03520.03170.3011-0.1114-0.0141-0.0512-0.0237-0.0049-0.02040.01960.0038-46.4567-20.48997.4971
161.30820.54170.3261.33570.09881.3116-0.08710.4304-0.0556-0.0806-0.05510.1456-0.06010.06620.1422-0.09960.0157-0.00450.0743-0.0449-0.0691-18.8555-0.513178.2957
171.84510.10510.34930.7576-0.14541.5565-0.19490.52910.0806-0.09070.123-0.1533-0.1530.18710.0718-0.092-0.04090.0080.18730.0189-0.126-15.36433.82470.229
180.92830.4344-0.1192.0430.51650.5938-0.11160.5539-0.0719-0.22870.11380.10350.0518-0.0921-0.0022-0.106-0.02790.01170.2978-0.0422-0.176-29.706-3.506565.7395
193.45620.25120.88920-0.08491.176-0.04030.0043-0.00390.0569-0.0230.0686-0.0757-0.12180.0633-0.00950.01130.034-0.0081-0.0397-0.0581-22.568-5.717987.7433
202.32540.1266-0.01160.91290.01041.5509-0.03660.5534-0.4809-0.08860.0615-0.11880.1824-0.0936-0.025-0.09690.0140.03670.0462-0.1152-0.0537-20.8357-12.021774.7219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|8 - A|47}A8 - 47
2X-RAY DIFFRACTION2{A|48 - A|113}A48 - 113
3X-RAY DIFFRACTION3{A|114 - A|189}A114 - 189
4X-RAY DIFFRACTION4{A|190 - A|226}A190 - 226
5X-RAY DIFFRACTION5{A|227 - A|292}A227 - 292
6X-RAY DIFFRACTION6{B|7 - B|46}B7 - 46
7X-RAY DIFFRACTION7{B|47 - B|144}B47 - 144
8X-RAY DIFFRACTION8{B|145 - B|192}B145 - 192
9X-RAY DIFFRACTION9{B|193 - B|216}B193 - 216
10X-RAY DIFFRACTION10{B|217 - B|292}B217 - 292
11X-RAY DIFFRACTION11{C|7 - C|100}C7 - 100
12X-RAY DIFFRACTION12{C|101 - C|144}C101 - 144
13X-RAY DIFFRACTION13{C|145 - C|182}C145 - 182
14X-RAY DIFFRACTION14{C|183 - C|217}C183 - 217
15X-RAY DIFFRACTION15{C|218 - C|292}C218 - 292
16X-RAY DIFFRACTION16{D|7 - D|62}D7 - 62
17X-RAY DIFFRACTION17{D|63 - D|144}D63 - 144
18X-RAY DIFFRACTION18{D|145 - D|185}D145 - 185
19X-RAY DIFFRACTION19{D|186 - D|226}D186 - 226
20X-RAY DIFFRACTION20{D|227 - D|292}D227 - 292

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