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- PDB-4k73: X-ray crystal structure of an L,D-transpeptidase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 4k73
TitleX-ray crystal structure of an L,D-transpeptidase from Mycobacterium tuberculosis H37Rv
ComponentsL,D-transpeptidase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / L / D-transpeptidase / transpeptidase
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / extracellular region
Similarity search - Function
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like ...Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable L,D-transpeptidase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of an L,D-transpeptidase from Mycobacterium tuberculosis H37Rv (CASP Target)
Authors: Lukacs, C.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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_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: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3862
Polymers29,3461
Non-polymers401
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.240, 46.440, 111.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L,D-transpeptidase


Mass: 29345.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_1433 / Production host: Escherichia coli (E. coli) / References: UniProt: O06825
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 E9: 0.2 M calcium chloride, 20% PEG3350, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 5.0.110.977408
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.54
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 26, 2013
RIGAKU SATURN 944+2CCDApr 2, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9774081
21.541
ReflectionResolution: 1.65→50 Å / Num. all: 28399 / Num. obs: 28136 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.23

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→46.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.872 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23077 1416 5 %RANDOM
Rwork0.19571 ---
obs0.19753 26663 99.08 %-
all-28399 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20 Å2
2---0.35 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 1 252 1897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0020.021576
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.942391
X-RAY DIFFRACTIONr_angle_other_deg0.92933624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.80723.13467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27215233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.744159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02393
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_it0.9221.362905
X-RAY DIFFRACTIONr_mcbond_other0.9221.361904
X-RAY DIFFRACTIONr_mcangle_it1.5472.0351133
X-RAY DIFFRACTIONr_scbond_it1.0941.467833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 106 -
Rwork0.269 1950 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -9.2092 Å / Origin y: 2.3378 Å / Origin z: -10.9587 Å
111213212223313233
T0.0438 Å2-0.0146 Å20.0106 Å2-0.0374 Å2-0.0139 Å2--0.0414 Å2
L1.6972 °2-0.1221 °20.3693 °2-0.1601 °2-0.103 °2--0.5965 °2
S-0.0244 Å °0.2222 Å °-0.0422 Å °-0.0641 Å °0.0159 Å °-0.0377 Å °-0.0092 Å °0.0023 Å °0.0085 Å °

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