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- PDB-5tr7: Crystal structure of a putative D-alanyl-D-alanine carboxypeptida... -

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Basic information

Entry
Database: PDB / ID: 5tr7
TitleCrystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsPENICILLIN-BINDING PROTEIN / PBP5 / penicil-binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / proteolysis
Similarity search - Function
D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRITE ION / DI(HYDROXYETHYL)ETHER / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase
B: D-alanyl-D-alanine carboxypeptidase
C: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,82511
Polymers112,1703
Non-polymers6558
Water1,45981
1
A: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,3901
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6944
Polymers37,3901
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5423
Polymers37,3901
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.749, 88.749, 85.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPHEPHEAA34 - 2813 - 250
21ALAALAPHEPHEBB34 - 2813 - 250
12ASPASPGLUGLUAA33 - 2832 - 252
22ASPASPGLUGLUCC33 - 2832 - 252
13ALAALAPHEPHEBB34 - 2813 - 250
23ALAALAPHEPHECC34 - 2813 - 250

NCS ensembles :
ID
3
1
2

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase


Mass: 37390.117 Da / Num. of mol.: 3 / Fragment: UNP residues 32-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: VC0947 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: A0A0H7A7Y4, UniProt: Q9KTF5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium Nitrate, 0.1 M Bis-Tris propane, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2016 / Details: 3.0 Undulator
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 47191 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.066 / Net I/σ(I): 36.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZO

1nzo


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 17.21 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23774 2246 4.8 %RANDOM
Rwork0.19086 ---
obs0.19321 44920 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.043 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å21.38 Å20 Å2
2--2.77 Å20 Å2
3----8.98 Å2
Refinement stepCycle: 1 / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 43 81 5896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195919
X-RAY DIFFRACTIONr_bond_other_d0.0010.025568
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9527982
X-RAY DIFFRACTIONr_angle_other_deg0.993312827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3245750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25925.305262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.942151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5731521
X-RAY DIFFRACTIONr_chiral_restr0.1320.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.026769
X-RAY DIFFRACTIONr_gen_planes_other0.0210.021326
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_it3.8443.6923006
X-RAY DIFFRACTIONr_mcbond_other3.8413.693005
X-RAY DIFFRACTIONr_mcangle_it4.9275.5213754
X-RAY DIFFRACTIONr_mcangle_other4.9275.5223755
X-RAY DIFFRACTIONr_scbond_it4.7894.1562913
X-RAY DIFFRACTIONr_scbond_other4.7844.1562913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.446.0614229
X-RAY DIFFRACTIONr_long_range_B_refined8.08644.1636629
X-RAY DIFFRACTIONr_long_range_B_other8.08644.166629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16068
12B16068
21A16224
22C16224
31B16066
32C16066
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 180 -
Rwork0.366 3271 -
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)
12.2201-2.1050.918810.5161.69732.42260.0437-0.2856-0.0940.60650.1675-0.21010.16370.1429-0.21120.1271-0.1051-0.03270.19280.01070.0232-37.696460.425616.215
20.3621-0.21610.61111.9092-0.27541.91210.06340.03870.0544-0.05840.0039-0.2124-0.20310.5247-0.06730.1295-0.14510.05120.2819-0.03210.159-33.006969.4326-3.599
32.25380.6742-2.64711.7143-0.77293.20930.03710.1624-0.1857-0.4728-0.1327-0.0293-0.086-0.07360.09560.409-0.032-0.01510.2604-0.07750.2405-37.1165.8926-17.7199
40.7558-0.39550.02091.78840.23853.16290.111-0.0102-0.0203-0.26330.0043-0.0846-0.06320.5632-0.11530.0834-0.05390.01950.1562-0.02170.0631-35.694567.3829-2.6703
52.8368-0.95840.26273.40230.7313.85990.02820.1047-0.26690.3904-0.0583-0.09440.15730.18860.03010.0894-0.0514-0.0180.09520.00220.0698-41.851959.26816.5494
63.1630.5245-1.79627.70055.7027.7383-0.0064-0.2432-0.35460.3551-0.18360.56430.21180.20210.18990.2229-0.09570.02780.20080.00590.2507-46.071857.935915.7676
72.72465.26110.627511.3019-2.096910.2702-0.2792-0.0588-0.1692-0.56360.3185-0.3504-0.3435-1.0252-0.03930.4755-0.03180.07250.3338-0.02250.1075-43.15152.6383-38.814
80.35860.38-0.85712.11310.62644.7114-0.0722-0.0759-0.0044-0.13010.5101-0.2711-0.38050.6524-0.43790.19190.0070.03350.4306-0.10110.3525-34.609236.6905-19.6736
91.25330.1084-2.56492.34091.34866.4332-0.04380.34370.06990.04130.13740.18270.0269-0.6626-0.09360.0640.05370.00620.37980.03420.2261-47.121233.6176-17.9311
102.7003-1.53231.4042.5325-0.01836.2-0.3179-0.0464-0.1725-0.28940.65040.2798-0.9328-1.0117-0.33250.28220.04560.00110.68520.10980.1786-50.097341.6824-25.897
111.94743.10441.61796.42883.72296.4712-0.3872-0.1965-0.122-1.14360.2877-0.1552-1.2758-0.67490.09950.3336-0.0453-0.00530.49050.01780.1848-45.026741.0255-32.6488
123.0031-0.85710.44568.69174.91075.4142-0.1471-0.23590.1728-0.28160.18850.3112-0.7884-0.9909-0.04150.4710.1761-0.02410.51940.12610.0775-48.563746.7222-35.3734
139.6772-2.0054-20.4583.71374.800943.3549-0.0988-0.71030.23410.61240.58880.13550.36011.5896-0.490.31340.0989-0.02750.1549-0.02650.3477-10.748727.6012-0.2541
140.7057-0.17840.15261.4752-1.15973.7185-0.0776-0.00860.05090.0219-0.2006-0.38170.32510.4160.27820.0580.04990.02820.10420.06520.69953.604437.3649-20.2604
150.8619-0.61330.25381.3223-0.3313.2538-0.10530.03110.2754-0.06-0.1056-0.32970.41270.34310.21090.09590.03830.04290.09070.06250.70792.317539.1195-24.5132
168.8396-4.3947-1.05284.3592.86973.0309-0.28430.04010.5041-0.2613-0.31310.1086-0.2113-0.63770.59730.2433-0.04750.03780.4288-0.13430.5093-10.271239.512-15.4431
170.23540.56750.40352.1004-0.00855.3408-0.0238-0.149-0.0618-0.0145-0.31950.03530.221-0.43710.34330.05020.0296-0.01280.1354-0.09150.6031-8.915233.712-11.2867
183.80021.3257-1.15398.26064.23893.17090.1574-0.3186-0.03670.2222-0.32050.29030.0099-0.1080.16310.0753-0.020.02340.2593-0.02470.3357-10.48439.51841.1193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 52
2X-RAY DIFFRACTION2A53 - 99
3X-RAY DIFFRACTION3A100 - 122
4X-RAY DIFFRACTION4A123 - 225
5X-RAY DIFFRACTION5A226 - 267
6X-RAY DIFFRACTION6A268 - 282
7X-RAY DIFFRACTION7B34 - 40
8X-RAY DIFFRACTION8B41 - 191
9X-RAY DIFFRACTION9B192 - 216
10X-RAY DIFFRACTION10B217 - 236
11X-RAY DIFFRACTION11B237 - 258
12X-RAY DIFFRACTION12B259 - 282
13X-RAY DIFFRACTION13C33 - 38
14X-RAY DIFFRACTION14C39 - 105
15X-RAY DIFFRACTION15C106 - 223
16X-RAY DIFFRACTION16C224 - 235
17X-RAY DIFFRACTION17C236 - 274
18X-RAY DIFFRACTION18C275 - 283

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