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- PDB-4rlb: Crystal structure of Acinetobacter baumannii CarO2 -

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Basic information

Entry
Database: PDB / ID: 4rlb
TitleCrystal structure of Acinetobacter baumannii CarO2
ComponentsCarbapenem-associated resistance protein
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel
Function / homology: / Porin - #170 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta / Carbapenem-associated resistance protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZahn, M. / Basle, A. / van den Berg, B.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Small-Molecule Transport by CarO, an Abundant Eight-Stranded beta-Barrel Outer Membrane Protein from Acinetobacter baumannii.
Authors: Zahn, M. / D'Agostino, T. / Eren, E. / Basle, A. / Ceccarelli, M. / van den Berg, B.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenem-associated resistance protein
B: Carbapenem-associated resistance protein


Theoretical massNumber of molelcules
Total (without water)55,2392
Polymers55,2392
Non-polymers00
Water00
1
A: Carbapenem-associated resistance protein


Theoretical massNumber of molelcules
Total (without water)27,6191
Polymers27,6191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbapenem-associated resistance protein


Theoretical massNumber of molelcules
Total (without water)27,6191
Polymers27,6191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.602, 139.602, 138.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 14 - 226 / Label seq-ID: 41 - 253

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carbapenem-associated resistance protein


Mass: 27619.365 Da / Num. of mol.: 2 / Fragment: UNP residues 22-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: carO / Production host: Escherichia coli (E. coli) / References: UniProt: Q5DL42

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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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 63% MPD, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→120.899 Å / Num. obs: 22490 / % possible obs: 99.9 %
Reflection shellResolution: 2.7→2.83 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
REFMAC5.8.0073refinement
XDSdata reduction
XDS/ XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→60 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.183 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22823 1071 4.8 %RANDOM
Rwork0.19022 ---
obs0.19203 21380 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.7→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 0 0 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023322
X-RAY DIFFRACTIONr_bond_other_d0.0050.023002
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9334524
X-RAY DIFFRACTIONr_angle_other_deg1.19436880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94525.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84115478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8021510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02808
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_it3.8144.4161702
X-RAY DIFFRACTIONr_mcbond_other3.8084.4141701
X-RAY DIFFRACTIONr_mcangle_it5.2436.6282124
X-RAY DIFFRACTIONr_mcangle_other5.2436.632125
X-RAY DIFFRACTIONr_scbond_it5.4355.0421620
X-RAY DIFFRACTIONr_scbond_other5.4355.0421620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.827.3742400
X-RAY DIFFRACTIONr_long_range_B_refined9.28937.8393650
X-RAY DIFFRACTIONr_long_range_B_other9.28837.8473651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10349 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 75 -
Rwork0.283 1533 -
obs--99.94 %
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)
10.9311-0.3802-0.3252.777-1.25763.07090.1527-0.17040.1092-0.15820.03310.1377-0.09680.14-0.18590.06310.01020.0470.1381-0.03850.1255-30.0928-46.54956.711
21.6432-3.3456-2.3628.06097.677610.3713-0.15630.1142-0.34110.2002-0.05540.66740.02760.2130.21170.0389-0.01140.0070.14780.03280.2031-15.5959-70.0169-5.2709
31.4433-1.3613-0.59421.3260.41041.15280.0279-0.214-0.0813-0.04570.23540.1282-0.12030.106-0.26330.119-0.04960.06210.16420.0460.2297-20.9872-53.8293-3.5383
41.4443-0.6394-0.42211.58380.71670.35290.0553-0.24740.3269-0.32130.1696-0.3785-0.13470.0533-0.22490.18960.0230.07410.23010.03270.1753-11.8081-58.9389-6.8733
55.5334-1.0299-2.46520.81610.46591.41490.30570.20470.1149-0.0851-0.098-0.1176-0.2301-0.0437-0.20770.07970.0120.06130.0802-0.02290.0977-11.9377-54.602-5.4182
63.08460.43030.55040.27750.25981.52910.0193-0.2911-0.11210.0781-0.0190.0069-0.1608-0.3643-0.00030.08690.0277-0.02050.1840.0590.107-45.6927-70.3491-48.759
77.1690.49134.57660.07030.24653.1777-0.0818-0.21680.3170.04730.00790.0376-0.0557-0.20230.07390.16260.0146-0.07340.02550.02270.1222-21.0143-70.8766-38.9051
82.707-0.64320.94220.2104-0.41431.22780.2825-0.2967-0.0271-0.02470.05390.04090.0863-0.205-0.33640.1738-0.0652-0.07950.16590.10780.1965-29.1301-75.2-36.0706
92.8565-2.46260.90146.8463-0.03611.91020.1049-0.335-0.12050.51960.03010.60770.1352-0.5371-0.1350.0856-0.05230.04070.23870.10990.2312-44.8459-71.3491-41.778
103.0535-0.67761.36510.8447-0.45250.97080.3793-0.422-0.4789-0.0659-0.0280.11330.1666-0.2351-0.35120.1126-0.0598-0.08110.12660.09490.138-26.6664-79.9777-36.7959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 48
2X-RAY DIFFRACTION2A49 - 68
3X-RAY DIFFRACTION3A69 - 121
4X-RAY DIFFRACTION4A122 - 196
5X-RAY DIFFRACTION5A197 - 226
6X-RAY DIFFRACTION6B14 - 54
7X-RAY DIFFRACTION7B55 - 76
8X-RAY DIFFRACTION8B77 - 142
9X-RAY DIFFRACTION9B143 - 160
10X-RAY DIFFRACTION10B161 - 226

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