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- PDB-5t1q: 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Ami... -

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Basic information

Entry
Database: PDB / ID: 5t1q
Title2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.
ComponentsN-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
KeywordsHYDROLASE / N-acetylmuramoyl-L-alanine Amidase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


amidase activity / extracellular region
Similarity search - Function
: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / CHAP domain profile. / CHAP domain / CHAP domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bagnoli, F. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bagnoli, F. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
B: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
C: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
D: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,45511
Polymers162,1674
Non-polymers2887
Water14,052780
1
A: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5883
Polymers40,5421
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5652
Polymers40,5421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7384
Polymers40,5421
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5652
Polymers40,5421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.570, 66.838, 102.737
Angle α, β, γ (deg.)108.70, 104.72, 90.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979


Mass: 40541.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02979 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q2G222
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: PACT (B2), 0.1M MIB (pH 5.0), 25% (w/v) PEG 1500

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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: Aug 11, 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: 2.15→30 Å / Num. obs: 82976 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 29.5
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.877 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FI7, 2LRJ

3fi7

2lrj


Resolution: 2.15→29.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.97 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 3806 4.6 %RANDOM
Rwork0.1732 ---
obs0.17524 78670 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.809 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.14 Å2-0.63 Å2
2--2.17 Å2-0.15 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11300 0 16 780 12096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210606
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.93415768
X-RAY DIFFRACTIONr_angle_other_deg0.86324499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8151436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04924.984612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.303151919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5121556
X-RAY DIFFRACTIONr_chiral_restr0.0840.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0213549
X-RAY DIFFRACTIONr_gen_planes_other0.0170.022801
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_it1.2762.535738
X-RAY DIFFRACTIONr_mcbond_other1.2742.535737
X-RAY DIFFRACTIONr_mcangle_it2.2453.7847176
X-RAY DIFFRACTIONr_mcangle_other2.2453.7847177
X-RAY DIFFRACTIONr_scbond_it1.2242.6765930
X-RAY DIFFRACTIONr_scbond_other1.2242.6765930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1173.9448593
X-RAY DIFFRACTIONr_long_range_B_refined4.77730.23513469
X-RAY DIFFRACTIONr_long_range_B_other4.69129.95213333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 256 -
Rwork0.22 5754 -
obs--97.28 %
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)
11.8622-0.93230.80361.12390.70072.21890.0852-0.4418-0.35690.22190.050.17040.4315-0.5055-0.13510.2745-0.0191-0.00350.2240.07990.1996-3.995-13.9172-9.065
21.68840.68640.28521.4348-0.21523.08350.0303-0.3078-0.02950.2652-0.1662-0.1054-0.4376-0.11660.13590.18610.0377-0.01710.13560.02150.01720.8519-0.0852-1.9557
31.64550.7539-0.09940.71630.17091.3562-0.03120.00890.09380.03570.01180.0593-0.077-0.09430.01940.04420.02450.01390.01660.0020.1387-4.238-10.9974-29.1511
41.5434-0.56891.10320.95130.96723.3870.1822-0.1579-0.20070.16430.04120.06070.5013-0.1786-0.22340.1639-0.00480.0220.08960.06660.0958-28.749112.5914-10.2234
51.90420.71270.57061.60840.37583.120.1196-0.40530.13450.3266-0.04990.0326-0.1033-0.1131-0.06970.10610.0070.02250.1237-0.01470.0228-24.810423.08111.1587
62.29970.32070.07991.0035-0.10271.1766-0.0241-0.00790.15340.01030.0460.0144-0.0636-0.0926-0.02190.02560.00470.01740.00970.00720.088-29.371920.877-28.835
71.46190.92210.08530.85951.02153.45060.00560.33160.2864-0.12320.16320.1325-0.4531-0.0604-0.16880.1378-0.02320.01680.18820.08980.12741.61922.497438.5271
81.9815-0.15430.74492.43551.01273.96710.02720.5425-0.1786-0.47480.3340.02470.28720.5249-0.36120.166-0.0425-0.04970.3005-0.06330.0446.73518.876431.0952
92.1183-0.52810.22140.93490.2871.4827-0.01660.0255-0.0404-0.01420.03970.0630.05750.0199-0.02310.0313-0.00540.02860.00780.01530.12030.959419.132558.9417
101.16150.1631-0.2930.81860.66913.56620.25860.1166-0.0061-0.1833-0.0329-0.0018-0.0255-0.1361-0.22560.14310.0368-0.00520.01720.01070.0568-22.568-10.954338.4531
111.4515-0.2268-0.34541.1534-0.36663.45190.17960.3302-0.0584-0.2344-0.0520.04290.15740.0769-0.12760.11720.0704-0.01280.0933-0.01720.0113-18.2633-12.562928.0824
123.5471-1.2285-0.11380.681-0.13121.02520.024-0.1334-0.2389-0.03550.0140.11190.0742-0.045-0.0380.02790.00140.02450.01540.0150.0957-23.5296-13.728958.4056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A262 - 306
2X-RAY DIFFRACTION2A307 - 483
3X-RAY DIFFRACTION3A484 - 619
4X-RAY DIFFRACTION4B261 - 312
5X-RAY DIFFRACTION5B313 - 484
6X-RAY DIFFRACTION6B485 - 619
7X-RAY DIFFRACTION7C261 - 306
8X-RAY DIFFRACTION8C307 - 485
9X-RAY DIFFRACTION9C486 - 619
10X-RAY DIFFRACTION10D262 - 332
11X-RAY DIFFRACTION11D333 - 483
12X-RAY DIFFRACTION12D484 - 619

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