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- PDB-7rjj: Crystal Structure of the Peptidoglycan Binding Domain of the Oute... -

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Basic information

Entry
Database: PDB / ID: 7rjj
TitleCrystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein (OmpA) from Klebsiella pneumoniae with bound D-alanine
ComponentsOmpA family protein
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Outer Membrane Protein
Function / homologyOuter membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / membrane => GO:0016020 / D-ALANINE / OmpA family protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpA family protein
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4666
Polymers28,2172
Non-polymers2494
Water3,189177
1
A: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2333
Polymers14,1091
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2333
Polymers14,1091
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.887, 41.887, 267.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein OmpA family protein


Mass: 14108.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: C4Z38_016670, EJ893_12145, I5002_15200, JMY88_11465 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 Magic / References: UniProt: A0A422WJQ0
#2: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.4 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: PEG's II (C4), 0.2M Magnesium chloride, 0.1M MES pH 6.5, 10% (w/v) PEG4000; Cryo: 0.2M Magnesium chloride, 0.1M MES pH 6.5, 25% (w/v) PEG4000

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2021 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 21507 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.023 / Rrim(I) all: 0.076 / Rsym value: 0.073 / Χ2: 0.837 / Net I/σ(I): 31.5
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.358 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1084 / CC1/2: 0.626 / CC star: 0.878 / Rpim(I) all: 0.439 / Rsym value: 1.358 / Χ2: 0.765 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→28.16 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.379 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 932 4.7 %RANDOM
Rwork0.2009 ---
obs0.2022 19054 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.21 Å2 / Biso mean: 22.826 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.88→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 14 178 2040
Biso mean--28.27 30.68 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131919
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171859
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6542602
X-RAY DIFFRACTIONr_angle_other_deg0.3611.594286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4975244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.66320.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14815314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3031520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0480.02424
LS refinement shellResolution: 1.882→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 26 -
Rwork0.274 562 -
all-588 -
obs--37.81 %
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)
11.9179-0.71090.54964.0068-0.12823.75630.04870.30950.2152-0.6018-0.0071-0.0546-0.2351-0.0345-0.04160.1927-0.00050.02440.06270.0580.0975-3.6928.19-13.835
25.2685-5.1188-1.16349.01342.5471.7181-0.1522-0.1049-0.04080.23420.0570.2839-0.0026-0.22410.09520.12940.03680.0330.07660.03930.1101-7.138.948-1.611
31.776-0.04720.47145.07590.09713.6729-0.02270.07810.086-0.10820.12120.20810.1953-0.4666-0.09840.11180.00170.01150.110.07550.0921-7.8842.585-7.542
43.1624-1.87680.66798.32981.12381.4937-0.1588-0.06560.3305-0.24490.1979-0.3512-0.1697-0.0104-0.03910.15520.03410.04770.02870.03830.1439-2.18313.563-5.835
52.86381.4252-0.85934.0973-0.82283.68570.0704-0.3488-0.29320.5767-0.0211-0.01370.2928-0.119-0.04930.20850.0032-0.02230.06560.05820.1089-4.21-8.55712.53
64.16514.02490.61698.17771.80791.2699-0.07630.0353-0.0204-0.16040.06440.1150.0331-0.18010.01180.1459-0.0404-0.01590.06910.0510.0994-5.621-8.0781.195
71.7280.1886-0.60485.22980.50734.45950.0016-0.099-0.1030.09320.08230.1833-0.1389-0.5156-0.08380.10270.0034-0.01620.11620.0820.1037-8.14-2.9746.049
83.07231.8726-0.56488.99291.10981.4018-0.18350.0965-0.35180.18980.2565-0.39170.1223-0.0129-0.07310.1419-0.0361-0.04220.03910.03850.1418-2.166-13.5574.547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A428 - 464
2X-RAY DIFFRACTION2A465 - 487
3X-RAY DIFFRACTION3A488 - 518
4X-RAY DIFFRACTION4A519 - 547
5X-RAY DIFFRACTION5B428 - 463
6X-RAY DIFFRACTION6B464 - 486
7X-RAY DIFFRACTION7B487 - 518
8X-RAY DIFFRACTION8B519 - 547

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