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- PDB-6muk: 1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from ... -

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Basic information

Entry
Database: PDB / ID: 6muk
Title1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae.
ComponentsPeptidase M23
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidase M23
Function / homologyPeptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Peptidase M23
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMinasov, G. / Shuvalova, L. / Pshenychnyi, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae.
Authors: Minasov, G. / Shuvalova, L. / Pshenychnyi, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2018ID: 6MOC
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2652
Polymers43,1991
Non-polymers651
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.964, 66.964, 181.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peptidase M23


Mass: 43199.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 700825 / FA 1090 / Gene: NGO_1686 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21.Gold / References: UniProt: Q5F676
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (C2), 1.1M Ammonium tartrate pH 7.0; Cryo: 4M Sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 32097 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Rsym value: 0.049 / Χ2: 1.01 / Net I/σ(I): 38.7
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1574 / CC1/2: 0.864 / Rpim(I) all: 0.33 / Rrim(I) all: 0.904 / Rsym value: 0.841 / Χ2: 1.001 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SLU

3slu


Resolution: 1.93→29.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.967 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23554 1606 5 %RANDOM
Rwork0.18849 ---
obs0.19079 30417 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.127 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: 1 / Resolution: 1.93→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 1 222 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132931
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172720
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6383971
X-RAY DIFFRACTIONr_angle_other_deg0.4081.5796266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.785381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.81820.366164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05615464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6081529
X-RAY DIFFRACTIONr_chiral_restr0.0560.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0470.02678
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_it1.8632.9281515
X-RAY DIFFRACTIONr_mcbond_other1.8592.9271514
X-RAY DIFFRACTIONr_mcangle_it2.8874.3721899
X-RAY DIFFRACTIONr_mcangle_other2.8874.3731900
X-RAY DIFFRACTIONr_scbond_it2.2393.1661416
X-RAY DIFFRACTIONr_scbond_other2.2353.1661416
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5664.6272073
X-RAY DIFFRACTIONr_long_range_B_refined7.11334.6113211
X-RAY DIFFRACTIONr_long_range_B_other7.09834.1653172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 121 -
Rwork0.28 2190 -
obs--100 %
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)
13.97570.9061-0.27655.05951.07356.9125-0.01820.2409-0.09880.2992-0.08370.6775-0.0385-0.74360.10190.069-0.03240.10910.1222-0.080.2271-19.084-39.919417.4308
21.71780.2595-0.31821.5281-0.32651.9074-0.14120.19920.03510.04790.02050.080.0447-0.05490.12070.0563-0.0508-0.03280.09190.00460.0644-1.7592-24.843413.6195
30.74450.4314-1.16012.0202-3.43136.4747-0.14540.02880.02890.2002-0.1303-0.2008-0.15670.47330.27570.1359-0.0263-0.05440.26630.02630.148916.8428-21.748923.4979
45.46063.08814.53742.02213.08024.73120.10450.2215-0.9730.33430.281-0.31220.61360.4985-0.38550.56190.07970.07730.37360.02450.49835.4083-40.325919.6691
50.5109-0.02680.48730.8603-1.45013.6974-0.1250.1203-0.05720.11370.0193-0.0511-0.06040.13340.10560.1212-0.01370.00270.04180.00330.06018.7643-25.796528.3032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 121
2X-RAY DIFFRACTION2A122 - 241
3X-RAY DIFFRACTION3A242 - 274
4X-RAY DIFFRACTION4A275 - 295
5X-RAY DIFFRACTION5A296 - 427

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