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- PDB-4v3h: Crystal structure of CymA from Klebsiella oxytoca -

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Basic information

Entry
Database: PDB / ID: 4v3h
TitleCrystal structure of CymA from Klebsiella oxytoca
ComponentsCYMA PROTEIN
KeywordsMEMBRANE / OUTER MEMBRANE CHANNEL CYCLODEXTRIN TRANSPORT BETA BARREL MONOMER
Function / homologyCyclodextrin porin CymA / Putative cyclodextrin porin / import into cell / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / NITRATE ION / CymA protein
Function and homology information
Biological speciesKLEBSIELLA OXYTOCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
Authorsvan den Berg, B. / Bhamidimarri, S.P. / Kleinekathoefer, U. / Winterhalter, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Outer-membrane translocation of bulky small molecules by passive diffusion.
Authors: van den Berg, B. / Prathyusha Bhamidimarri, S. / Dahyabhai Prajapati, J. / Kleinekathofer, U. / Winterhalter, M.
History
DepositionOct 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Feb 21, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYMA PROTEIN
B: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,16317
Polymers79,8112
Non-polymers4,35215
Water10,016556
1
A: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0518
Polymers39,9061
Non-polymers2,1457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1139
Polymers39,9061
Non-polymers2,2078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.211, 61.430, 108.237
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYMA PROTEIN


Mass: 39905.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CLONING REGION INCLUDING HEPTAHISTIDINE TAG AT N-TERMINUS
Source: (gene. exp.) KLEBSIELLA OXYTOCA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 DELTA CYOABCD / References: UniProt: Q48391
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.55 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8
Details: 23% PEG2000 0.1 M TRIS PH 8 0.3 M MAGNESIUM NITRATE HEXAHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 77325 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V3G
Resolution: 1.83→43.353 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 1753 2.6 %
Rwork0.1742 --
obs0.175 67180 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→43.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5178 0 192 556 5926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065577
X-RAY DIFFRACTIONf_angle_d1.0797474
X-RAY DIFFRACTIONf_dihedral_angle_d18.7042144
X-RAY DIFFRACTIONf_chiral_restr0.044709
X-RAY DIFFRACTIONf_plane_restr0.004967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87950.23131230.20564553X-RAY DIFFRACTION86
1.8795-1.93480.2211260.1894656X-RAY DIFFRACTION88
1.9348-1.99730.19911330.16564775X-RAY DIFFRACTION90
1.9973-2.06860.18631300.1574859X-RAY DIFFRACTION92
2.0686-2.15150.19651350.15774955X-RAY DIFFRACTION94
2.1515-2.24940.18141360.15955065X-RAY DIFFRACTION95
2.2494-2.3680.19521410.17165079X-RAY DIFFRACTION96
2.368-2.51630.21111340.1735103X-RAY DIFFRACTION96
2.5163-2.71060.22071460.17595174X-RAY DIFFRACTION97
2.7106-2.98330.21851330.17935235X-RAY DIFFRACTION98
2.9833-3.41480.221400.1745269X-RAY DIFFRACTION99
3.4148-4.30170.1911370.16315303X-RAY DIFFRACTION99
4.3017-43.36540.21441390.19115401X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.10260.08430.02430.55140.35550.773-0.03760.1187-0.1442-0.01750.01480.03980.0045-0.00020.0130.08030.0156-0.00380.1469-0.01310.2021-25.16658.6165-48.2256
22.11620.3053-0.43390.2496-0.10230.56970.09550.05620.02760.08270.0373-0.15510.06080.035-0.13220.08130.0124-0.01070.1574-0.04210.2161-24.71584.8307-41.5081
34.4652-2.039-0.40141.70110.3560.83280.10110.1073-0.1431-0.0345-0.0750.06840.0741-0.0413-0.06320.1078-0.01240.00750.14470.0150.1904-35.03777.6955-35.3721
42.7196-1.0988-0.64611.46290.31720.68250.07530.1752-0.45740.041-0.11680.13990.05860.03920.01910.1017-0.0051-0.03760.1607-0.01360.1616-26.34358.1914-35.3215
52.6559-1.64990.66432.3183-0.71990.91050.09930.1211-0.2891-0.0001-0.05260.09930.0780.0663-0.05090.1-0.0025-0.0040.1463-0.00550.1369-24.202711.0953-31.8521
60.4937-0.28880.22060.9337-0.5051.34370.0127-0.0319-0.08420.06570.04910.053-0.014-0.0587-0.08440.0679-0.016-0.00060.10060.01830.1322-23.610419.0857-36.4544
70.1933-0.0942-0.22350.8079-0.00770.48330.0394-0.06320.06430.0089-0.11190.01160.12890.03930.07220.1141-0.01430.01420.13250.0250.1801-16.075618.6227-38.2695
81.2591-0.0949-0.31261.09160.28250.75580.06630.01240.1111-0.0260.0696-0.0987-0.13760.0411-0.1180.1439-0.0370.03780.1193-0.01760.1596-41.48128.3586-13.7477
90.6243-0.16780.44761.40240.19980.6586-0.03350.12620.1563-0.19460.0739-0.0805-0.21690.11020.09020.1986-0.07290.05410.1499-0.00040.1595-44.508732.587-19.4638
102.08820.9911-0.08972.2023-0.19070.8965-0.0752-0.01750.0511-0.1947-0.0089-0.185-0.11820.06910.02820.1585-0.02460.03620.12540.00920.1493-45.393136.6621-19.9626
111.2060.6120.98112.08190.72411.1616-0.10390.19050.3006-0.13220.08560.0541-0.12950.12510.06560.1647-0.01850.04150.14-0.00950.2085-42.500844.3445-16.2224
123.88190.82181.7540.43530.70641.43860.04090.137-0.463-0.02110.0532-0.0455-0.0934-0.0016-0.08810.166-00.0180.1686-0.07520.3456-42.487445.6732-10.1807
130.22290.02440.43160.94610.17131.35250.10610.2704-0.4141-0.0473-0.09570.2630.111-0.1767-0.0870.1782-0.00650.0140.232-0.1190.455-49.991642.6999-9.1625
140.1777-0.28680.32441.82320.30841.07310.05780.1768-0.2290.0925-0.03920.1019-0.0188-0.0962-0.04970.1464-0.00550.01890.1856-0.06920.2492-44.171940.6298-3.6632
150.77430.68890.13850.8277-0.07980.28130.10170.13540.15880.02630.0383-0.0957-0.0423-0.0331-0.0040.14150.0137-0.01780.1687-0.0380.1376-37.029832.5754-4.1473
160.63220.57560.47571.21820.15330.46160.1364-0.00090.26010.3162-0.03890.10880.0329-0.2069-0.1880.1763-0.00180.08190.21530.00130.2154-47.779633.6021-1.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 11 THROUGH 123 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 124 THROUGH 146 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 147 THROUGH 165 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 166 THROUGH 187 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 188 THROUGH 230 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 231 THROUGH 297 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 298 THROUGH 324 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 18 THROUGH 82 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 83 THROUGH 103 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 104 THROUGH 146 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 147 THROUGH 187 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 188 THROUGH 206 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 207 THROUGH 230 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 231 THROUGH 277 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 278 THROUGH 297 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 298 THROUGH 324 )

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