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- PDB-4xin: X-ray Crystal Structure of an LpqH orthologue from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 4xin
TitleX-ray Crystal Structure of an LpqH orthologue from Mycobacterium avium
ComponentsLpqH orthologue
KeywordsUNKNOWN FUNCTION / SSGCID / LpqH / Mycobacterium avium / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology19kDa lipoprotein antigen / Mycobacterium 19 kDa lipoprotein antigen / membrane / LpqH orthologue / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.5 Å
AuthorsFairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: X-ray Crystal Structure of an LpqH orthologue from Mycobacterium avium
Authors: Fairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LpqH orthologue
B: LpqH orthologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1453
Polymers27,1222
Non-polymers231
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-21 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.030, 37.630, 41.960
Angle α, β, γ (deg.)110.120, 95.970, 97.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LpqH orthologue


Mass: 13561.138 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria)
Strain: 104 / Gene: MAV_0969 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QBE0, UniProt: A0A0J9X263*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ well H9 - 0.2 M Lithium sulfate, 25% PEG3350, 0.1 M BIS-TRIS pH 5.50; MyavA.18632.a.B2 PS02022 at 25.7mg/ml
PH range: 5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.97624
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.54
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDAug 21, 2014
RIGAKU SATURN 944+2CCDAug 27, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976241
21.541
ReflectionNumber: 75991 / Rmerge(I) obs: 0.019 / Χ2: 1.79 / D res high: 2.1 Å / Num. obs: 20228 / % possible obs: 95.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
6.649.3938810.02
5.426.6453310.017
4.75.4263810.017
4.24.772010.019
3.834.281910.018
3.553.8388810.018
3.323.5595210.018
3.133.32101010.019
2.973.13106110.018
2.832.97112210.018
2.712.83114110.019
2.62.71124310.019
2.512.6118010.02
2.422.51135310.021
2.352.42133110.021
2.282.35135110.021
2.212.28140610.022
2.152.21146810.022
2.12.15140910.023
ReflectionResolution: 1.5→50 Å / Num. obs: 27430 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 14.72 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.046 / Χ2: 0.992 / Net I/σ(I): 17.22 / Num. measured all: 79785
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.540.9560.2015.695811213020000.24793.9
1.54-1.580.9720.1616.955928212020000.19694.3
1.58-1.630.9750.1467.735663200919060.17994.9
1.63-1.680.9830.1258.735574198318810.15394.9
1.68-1.730.9870.10910.275242189317820.13394.1
1.73-1.790.9890.08812.195150186517610.10894.4
1.79-1.860.9920.07513.594916177116720.09394.4
1.86-1.940.9940.06216.344662169816010.07794.3
1.94-2.020.9970.04719.714513166915620.05793.6
2.02-2.120.9960.04321.924201155414570.05493.8
2.12-2.240.9970.03923.194094148914260.04895.8
2.24-2.370.9970.03724.473882141713500.04695.3
2.37-2.540.9970.03724.833676133712740.04595.3
2.54-2.740.9970.03426.253404123211810.04295.9
2.74-30.9970.03228.163181113911000.0496.6
3-3.350.9980.03129.562885103210030.03897.2
3.35-3.870.9980.0330.4325269118850.03697.1
3.87-4.740.9980.02730.4621087727500.03397.2
4.74-6.710.9980.02830.5516035915640.03495.4

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.5→31.391 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1362 4.97 %RANDOM
Rwork0.1601 26064 --
obs0.1617 27426 94.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.42 Å2 / Biso mean: 23.3018 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.5→31.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 1 185 1815
Biso mean--21.66 30.13 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091726
X-RAY DIFFRACTIONf_angle_d1.2462360
X-RAY DIFFRACTIONf_chiral_restr0.056277
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d11.11635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.55370.24231350.19072575271094
1.5537-1.61590.2161250.18692629275495
1.6159-1.68950.2061250.18072611273695
1.6895-1.77850.20441430.16982597274095
1.7785-1.890.22321410.17972572271395
1.89-2.03590.18951590.15422526268593
2.0359-2.24070.2021530.15292612276595
2.2407-2.56480.2061200.16492617273796
2.5648-3.23080.191260.16532694282097
3.2308-31.39830.17281350.1442631276696
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)
15.30650.17122.44936.9406-2.04949.2830.4955-0.7567-0.54280.22540.3698-0.22790.36910.0774-0.79480.1924-0.0678-0.02160.4297-0.02040.3538-3.6833-2.899238.2445
26.68332.1916-0.99142.274-0.41561.72860.2108-1.2607-0.01810.2497-0.3564-0.13530.21970.09330.1550.2003-0.0413-0.01410.27540.01220.1428.80943.377240.3876
36.32860.24242.51246.22070.98748.67590.14760.40030.1199-0.05370.22041.275-0.4786-0.2337-0.21420.15260.02090.01380.24080.05290.5011-4.72935.796631.562
43.95421.3562.34264.50871.21932.31740.05550.56580.2335-0.3839-0.29570.8625-0.012-0.7520.10940.16380.0421-0.07120.3018-0.00080.3342-1.32356.315526.4024
53.84840.59090.33616.81395.52045.6518-0.1143-0.11970.3713-0.4101-0.21280.6974-0.8435-0.30220.39220.18430.0166-0.03420.13530.01840.23743.250210.247330.8376
63.17131.23650.22924.05961.28653.8234-0.0730.3519-0.1382-0.2349-0.08690.32670.1918-0.22790.11510.13790.0085-0.00830.1266-0.00680.16338.37466.921726.5463
76.77885.9485-2.16486.9387-2.43132.1497-0.1630.3108-0.2841-0.32390.08530.0150.1238-0.08930.07040.15280.0243-0.01660.1545-0.01810.17339.54530.15624.3604
82.62682.9778-0.0366.26421.02961.21120.1419-0.1412-0.15750.2366-0.1359-0.13240.0229-0.0584-0.05180.10980.0234-0.03740.11180.03830.122213.72347.445233.2668
92.05611.5295-0.61794.2698-0.42330.64020.0359-0.0403-0.34010.0909-0.0694-0.2418-0.0037-0.05770.02180.10050.0223-0.02130.08610.02140.080412.89196.536233.6644
104.3241-1.5551-2.33810.9250.81821.15740.12790.66240.4013-0.77580.2035-0.1172-0.7447-0.4555-0.19920.3195-0.07880.0280.19710.02560.10718.357530.505816.4547
114.9493-3.6192-6.41075.02824.27518.38430.1044-0.22950.5598-0.29460.2776-0.3741-0.46010.3704-0.40280.153-0.0293-0.02320.1364-0.00770.179318.74832.839625.5301
123.74033.00074.02812.90954.20226.1008-0.17980.7132-0.6352-0.65250.4508-0.71980.07050.2344-0.23190.3005-0.01140.05580.2437-0.04780.254720.131419.171413.9508
135.14120.33521.60954.11051.76923.09480.06730.5042-0.6879-0.7216-0.049-0.20810.3894-0.31330.05970.3041-0.0653-0.01450.2382-0.00870.131214.967517.072215.6835
143.16950.21650.56082.64640.42263.3711-0.07760.5278-0.1636-0.47330.08330.20730.0385-0.2435-0.03670.1566-0.0149-0.05420.16470.02040.111211.28319.152320.1701
156.27651.43491.29183.55050.82522.6696-0.06440.07810.1368-0.14990.00240.46120.0143-0.33420.05580.12770.0155-0.03290.13050.03830.1458.677521.58328.5053
166.26731.9433-6.1011.5091-1.57695.99320.39130.6437-0.5755-0.5641-0.3360.5080.2839-0.7779-0.14710.39970.0605-0.09240.413-0.00970.18626.859526.992112.2106
171.7422-0.0495-0.59162.7895-0.90143.94150.04440.02020.030.0533-0.0160.0594-0.2177-0.0755-0.01990.0905-0.0023-0.0170.07650.0040.093111.451326.855928.1158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 17 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 38 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 47 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 58 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 82 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 96 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 111 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 112 through 126 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 23 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 24 through 30 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 38 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 48 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 49 through 72 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 73 through 88 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 96 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 97 through 126 )B0

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