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- PDB-4c4v: Structure of the outer membrane protein insertase BamA with one P... -

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Basic information

Entry
Database: PDB / ID: 4c4v
TitleStructure of the outer membrane protein insertase BamA with one POTRA domain.
Components(OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA) x 2
KeywordsPROTEIN TRANSPORT / OMP85 SUPERFAMILY
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain ...membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZeth, K. / Albrecht, R. / Diederichs, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of Bama, an Essential Factor in Outer Membrane Protein Biogenesis
Authors: Albrecht, R. / Schuetz, M. / Oberhettinger, P. / Faulstich, M. / Bermejo, I. / Rudel, T. / Diederichs, K. / Zeth, K.
History
DepositionSep 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references / Source and taxonomy
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-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: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
B: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA


Theoretical massNumber of molelcules
Total (without water)104,6102
Polymers104,6102
Non-polymers00
Water2,180121
1
A: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA


Theoretical massNumber of molelcules
Total (without water)52,1411
Polymers52,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA


Theoretical massNumber of molelcules
Total (without water)52,4691
Polymers52,4691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.583, 67.347, 109.795
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA / OMP85


Mass: 52140.750 Da / Num. of mol.: 1
Fragment: BAMA TRUNCATED BY 4 POTRA DOMAINS, RESIDUES 347-808
Source method: isolated from a genetically manipulated source
Details: OUTER MEMBRANE PROTEIN BAMA FROM E. COLI TRUNCATED BY POTRA DOMAIN 1
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A940
#2: Protein OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA / OMP85


Mass: 52469.102 Da / Num. of mol.: 1
Fragment: BAMA TRUNCATED BY 4 POTRA DOMAINS, RESIDUES 344-808
Source method: isolated from a genetically manipulated source
Details: OUTER MEMBRANE PROTEIN BAMA FROM E. COLI TRUNCATED BY POTRA DOMAIN 1
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A940
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.94 Å3/Da / Density % sol: 58.17 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47 Å / Num. obs: 28588 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 91.63 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.2
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→33.59 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.8437 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.471
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1178 5.02 %RANDOM
Rwork0.2335 ---
obs0.2365 23451 99.59 %-
Displacement parametersBiso mean: 93.98 Å2
Baniso -1Baniso -2Baniso -3
1--25.5698 Å20 Å26.377 Å2
2--5.861 Å20 Å2
3---19.7088 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 3→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 0 121 7144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087219HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.159807HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2374SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1065HARMONIC5
X-RAY DIFFRACTIONt_it7219HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion24.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion885SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7513SEMIHARMONIC4
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3271 146 5.13 %
Rwork0.2554 2702 -
all0.2591 2848 -
obs--99.59 %
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)
11.49372.6826-1.787200.41171.33720.0097-0.03150.0177-0.0662-0.0117-0.0975-0.0113-0.03390.0021-0.0885-0.1469-0.09430.1214-0.0888-0.094771.53650.109772.41
22.68692.1031-2.818200.03442.82490.0093-0.0016-0.0342-0.318-0.0352-0.0223-0.0811-0.00360.0259-0.1278-0.1311-0.14110.24690.0085-0.160572.10676.520669.9944
3-0.3170.84542.6253.39560.70844.7389-0.0113-0.55920.0426-0.01450.0648-0.12380.03160.3061-0.05350.26710.13640.02150.10210.0135-0.239440.54689.912151.3061
40.2780.4495-2.33812.23592.03162.6666-0.067-0.48150.05350.55410.1872-0.14620.5496-0.1127-0.12020.3201-0.0482-0.1143-0.3036-0.0201-0.320129.12980.53249.739
50.94680.2916-0.43192.56910.55824.27970.06490.1149-0.24830.5409-0.1111-0.07790.5465-0.52950.04620.2894-0.0058-0.1161-0.304-0.0207-0.319825.974-1.240734.4231
61.76281.8146-0.96015.0747-0.13076.15870.04390.22070.2992-0.20930.22490.1096-0.1978-0.2263-0.26890.27410.1257-0.0011-0.3040.0458-0.306231.19169.920225.0281
77.1185-0.99112.23591.2248-2.11587.4671-0.01290.04520.02870.26030.0489-0.01690.05540.136-0.036-0.28570.1522-0.15090.3032-0.0443-0.322376.9243-30.0527-11.2821
80.0048-0.164-0.09391.30930.12111.80220.09850.5069-0.4396-0.13750.1068-0.0053-0.07440.5248-0.2053-0.0281-0.0535-0.07640.1173-0.0714-0.165141.8948-32.05693.4539
90.2180.9221-1.82590.03012.08910.7745-0.00180.01170.0453-0.0158-0.0178-0.0742-0.00920.05670.01960.1399-0.120.1050.069-0.1539-0.034947.7953-15.39450.309
101.63870.69181.16373.33991.15264.52080.25160.16130.128-0.5317-0.08280.0458-0.5204-0.5306-0.16880.29770.09560.0697-0.3040.0056-0.297727.6929-22.291511.9837
110.26331.3073-1.39940-2.5611-0.10920.0174-0.0106-0.04390.0144-0.02260.10560.0658-0.17460.00520.05210.05110.08740.06510.0426-0.1369.2816-30.37517.6543
123.5493-1.73471.42034.1374-0.48217.63660.0869-0.3963-0.03760.43870.1279-0.0762-0.1983-0.5504-0.21480.1819-0.1002-0.0296-0.3040.0387-0.29229.3637-29.082828.5421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|347 - 364}
2X-RAY DIFFRACTION2{A|365 - 427}
3X-RAY DIFFRACTION3{A|428 - 460}
4X-RAY DIFFRACTION4{A|461 - 547}
5X-RAY DIFFRACTION5{A|548 - 764}
6X-RAY DIFFRACTION6{A|765 - 808}
7X-RAY DIFFRACTION7{B|344 - 427}
8X-RAY DIFFRACTION8{B|428 - 478}
9X-RAY DIFFRACTION9{B|479 - 488}
10X-RAY DIFFRACTION10{B|489 - 678}
11X-RAY DIFFRACTION11{B|698 - 708}
12X-RAY DIFFRACTION12{B|709 - 808}

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