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- PDB-6v45: Crystal structure of a Probable carnitine operon oxidoreductase c... -

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Basic information

Entry
Database: PDB / ID: 6v45
TitleCrystal structure of a Probable carnitine operon oxidoreductase caia from Brucella melitensis
ComponentsProbable carnitine operon oxidoreductase caia
KeywordsOXIDOREDUCTASE / SSGCID / Probable carnitine operon oxidoreductase caia / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / transferase activity / oxidoreductase activity
Similarity search - Function
: / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain
Similarity search - Domain/homology
Probable carnitine operon oxidoreductase caia
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Probable carnitine operon oxidoreductase caia from Brucella melitensis
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable carnitine operon oxidoreductase caia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5573
Polymers23,3651
Non-polymers1922
Water23413
1
A: Probable carnitine operon oxidoreductase caia
hetero molecules

A: Probable carnitine operon oxidoreductase caia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1136
Polymers46,7292
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area11280 Å2
ΔGint-129 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.060, 96.060, 96.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z

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Components

#1: Protein Probable carnitine operon oxidoreductase caia


Mass: 23364.600 Da / Num. of mol.: 1 / Fragment: BrmeA.18116.b.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0848 / Plasmid: BrmeA.18116.b.B2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q8YHF3, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Optimization screen around condition Anatrace MCSG1_E6, well C4: 18.9% (w/V) PEG 3350, 200mM Potassium sulfate: BrmeA.18116.b.B2.PS01846 at 18.1mg/ml: tray 312854c4, cryo: 20% EG in 2 steps: puck xvm4-2.

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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: RAYONIX MX-300 / Detector: CCD / Date: Oct 30, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9354 / % possible obs: 99.9 % / Redundancy: 7.36 % / Biso Wilson estimate: 71.381 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.047 / Χ2: 1.051 / Net I/σ(I): 27.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.5110.63937000.8620.687100
2.67-2.747.5650.4983.876480.9020.535100
2.74-2.827.5370.3775.26550.9420.405100
2.82-2.917.4870.2677.236120.9780.287100
2.91-37.5230.2059.566140.9840.22100
3-3.117.4970.15212.365790.990.163100
3.11-3.237.4420.10817.715730.9950.116100
3.23-3.367.4580.07424.765550.9970.08100
3.36-3.517.3890.06727.165120.9980.072100
3.51-3.687.4330.05532.565170.9990.059100
3.68-3.887.3760.0440.94890.9990.043100
3.88-4.117.3270.03447.234530.9990.037100
4.11-4.47.2410.03152.084320.9990.034100
4.4-4.757.2110.03153.934020.9990.033100
4.75-5.27.2210.02956.53670.9990.031100
5.2-5.827.1690.02855.583490.9990.03100
5.82-6.727.1470.02657.533060.9990.028100
6.72-8.226.9150.02359.1425910.025100
8.22-11.636.7090.01965.132060.9990.02199.5
11.63-505.6190.02258.961260.9980.02496.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A

Resolution: 2.6→42.96 Å / SU ML: 0.3552 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.124
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 934 9.99 %0
Rwork0.1986 ---
obs0.2023 9352 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 88.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 10 13 1274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481291
X-RAY DIFFRACTIONf_angle_d0.70771757
X-RAY DIFFRACTIONf_chiral_restr0.0517186
X-RAY DIFFRACTIONf_plane_restr0.0043230
X-RAY DIFFRACTIONf_dihedral_angle_d27.0533465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.34941510.29511162X-RAY DIFFRACTION100
2.74-2.910.4091240.32451203X-RAY DIFFRACTION100
2.91-3.130.31061150.281189X-RAY DIFFRACTION100
3.13-3.450.26121210.23711205X-RAY DIFFRACTION100
3.45-3.950.28641530.20441179X-RAY DIFFRACTION100
3.95-4.970.19011290.15271210X-RAY DIFFRACTION100
4.97-42.960.17941410.16921270X-RAY DIFFRACTION99.72
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)
10.842505963538-1.4813632739-2.271749476184.513827082931.767767693098.70881472790.0161715273559-0.3135848301470.290253650573-0.6413443530170.611602661907-0.817430894206-0.06566148178660.969134952107-0.5312085336250.92683446989-0.2578089473620.08147600175681.87815018353-0.6393690223530.69662051005515.01854512913.139278020234.5507941127
20.7630363878610.10392372606-0.0296486130883.383394875750.5764738652561.24200209695-0.5705873316550.182649400543-0.0194623209409-0.3434297564330.640947589281-0.1381787492560.0480152170058-0.7466505873030.04484849480410.399128354527-0.135605195371-0.01540551777831.66805445213-0.5419807021920.55386147836413.0858204582-0.77438441133344.2093924567
31.30807081566-0.05877486314770.7359201069534.39919975369-3.886815908583.79160686171-0.240300239267-0.11114846833-0.2804803322721.00596989060.303387779958-1.028388322340.156635338211.05288686446-0.5411647535470.7006684243290.0698285009039-0.06559606336111.49333417246-0.6113527700180.74167629540817.66570147499.4496668283259.3924653515
41.21225578496-1.09961529142-1.259133721932.976524041341.831564373264.07204329948-0.09795943834160.345763353242-0.1271592671040.2770021025140.228211105494-0.56083856737-0.416509461812-0.5009406497810.06057039140060.6656801056340.414293329829-0.2887098891620.988864334159-0.6572374951390.64295153788222.621768299824.858305985260.2370100833
50.4380895529631.069532305440.614760379192.878889009690.6759273482522.82432847039-0.6532147577850.442667767559-0.083858048962-0.1680911219150.208570043692-0.194520714971-0.507574287707-1.07237238304-0.1094805655090.6166101242580.266562505556-0.0949346817031.5310302896-0.518729014340.66958059532517.078260012820.29003074249.9559859046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 125 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 124 )

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