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- PDB-5w1g: CR1-07 unliganded Fab -

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Basic information

Entry
Database: PDB / ID: 5w1g
TitleCR1-07 unliganded Fab
Components
  • CR1-07 Fab heavy chain
  • CR1-07 Fab light chain
KeywordsIMMUNE SYSTEM / Fab / antibody / Machupo virus / Junin virus / arenavirus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRaymond, D.D. / Clark, L.E. / Abraham, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI007061 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI109740 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP5OD023084 United States
Other private United States
Other private United States
CitationJournal: Nat Commun / Year: 2018
Title: Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.
Authors: Clark, L.E. / Mahmutovic, S. / Raymond, D.D. / Dilanyan, T. / Koma, T. / Manning, J.T. / Shankar, S. / Levis, S.C. / Briggiler, A.M. / Enria, D.A. / Wucherpfennig, K.W. / Paessler, S. / Abraham, J.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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
H: CR1-07 Fab heavy chain
L: CR1-07 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,4092
Polymers48,4092
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-23 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.770, 137.410, 78.670
Angle α, β, γ (deg.)90.000, 148.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-326-

HOH

21H-414-

HOH

31L-404-

HOH

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Components

#1: Antibody CR1-07 Fab heavy chain


Mass: 24016.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Production host: Homo sapiens (human)
#2: Antibody CR1-07 Fab light chain


Mass: 24392.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.5
Details: 19% (v/v) polyethylene glycol monomethyl ether 550, MES pH 6.5 and, 10 mM zinc sulfate heptahydrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→44.214 Å / Num. obs: 32753 / % possible obs: 96.3 % / Redundancy: 4.48 % / Biso Wilson estimate: 34.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.138 / Χ2: 0.945 / Net I/σ(I): 9.57 / Num. measured all: 146726
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.124.571.0221.6523888541652270.6461.16196.5
2.12-2.264.4980.7332.4621591494348000.7530.83597.1
2.26-2.444.310.4743.7720008483046420.8720.54396.1
2.44-2.684.6250.2766.4520507456244340.9590.31397.2
2.68-2.994.4660.14510.4716919394837880.9850.16595.9
2.99-3.454.3860.08416.1914946356034080.9940.09695.7
3.45-4.224.5130.06720.913145301629130.9950.07696.6
4.22-5.944.4170.05625.059996237122630.9960.06395.4
5.94-44.2144.480.05327.065726137112780.9960.06193.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.214 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 1638 5.01 %RANDOM
Rwork0.2308 31079 --
obs0.2333 32717 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.21 Å2 / Biso mean: 53.0813 Å2 / Biso min: 18.37 Å2
Refinement stepCycle: final / Resolution: 2→44.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 0 223 3601
Biso mean---44.87 -
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.0590.4391340.40842545267996
2.059-2.12550.40211390.34532630276999
2.1255-2.20140.39121350.34492559269499
2.2014-2.28960.35811360.33252590272698
2.2896-2.39380.37051340.31162535266997
2.3938-2.520.34111380.2972618275699
2.52-2.67780.33451370.27012619275698
2.6778-2.88460.31661360.24782566270298
2.8846-3.17480.29891350.23272567270296
3.1748-3.6340.25421370.20082605274299
3.634-4.57770.21331370.16252595273298
4.5777-44.22480.21051400.18032650279099
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)
12.18330.69520.32782.3449-0.31491.84440.0446-0.016-0.22090.41020.0775-0.02840.14930.5241-0.0320.37490.0528-0.02010.2916-0.04540.342334.483416.536923.1806
21.3047-2.0184-0.82184.0986-0.35323.44310.05570.0876-0.1236-0.1009-0.11690.30030.5-0.76130.11980.3698-0.03440.01380.281-0.0330.288421.391414.933618.6402
32.00090.5717-0.26132.0539-0.69381.92940.1004-0.1109-0.08580.4337-0.03430.0585-0.05240.2325-0.01150.36550.03770.01740.2646-0.03730.22230.130423.342827.3414
41.1851.3942-0.25444.9201-2.31012.52360.1978-0.09-0.16420.1225-0.12210.33680.26510.2274-0.13110.34550.04070.00930.2726-0.05640.265826.089814.370721.125
51.11350.5482-0.28041.694-0.46191.2011-0.00370.0065-0.03520.0416-0.05570.112-0.01580.21080.06930.22-0.02250.02720.2415-0.03860.24130.74122.869515.1033
63.375-3.851-2.17068.04251.24933.9119-0.41410.2807-0.30690.7267-0.03140.6213-0.5069-0.1550.30220.33110.0148-0.0870.3001-0.00420.336827.3579-7.378829.95
72.73810.0304-2.5931.6969-0.45362.57170.29830.12880.1943-0.48630.44850.20310.23670.5344-0.60050.39330.02870.00340.41070.01470.28932.7815-19.950111.3124
81.4705-0.1658-0.20471.33470.33681.8525-0.219-0.03090.0184-0.02010.0964-0.1282-0.08890.160.1560.3098-0.0212-0.00770.2487-0.00490.255732.8081-11.382914.7454
90.35830.21560.60882.87451.37831.5227-0.0522-0.09390.0733-0.1671-0.0132-0.3918-0.3390.51120.06120.3883-0.0241-0.0450.39030.00260.303137.0068-6.374125.8126
100.61220.53280.83074.95874.56544.41050.1384-0.3785-0.19680.33030.084-0.29840.7429-0.3019-0.16310.4367-0.0649-0.00080.51680.0380.267837.9567-25.578813.6306
112.0523-1.08-0.69076.98114.29434.2178-0.0728-0.1385-0.2279-0.11290.0603-0.01610.5121-0.14450.13630.3479-0.1025-0.02810.30510.06190.260613.138414.51935.2948
122.8411-2.2125-2.44183.51022.79294.29110.380.4392-0.0591-0.2237-0.3351-0.1085-0.0455-0.4067-0.02350.37160.0631-0.04840.33340.0140.284515.64315.3964-2.4646
132.06613.6322-0.88946.5309-1.61460.40490.0356-0.04620.4020.2592-0.05230.1464-0.61450.0624-0.08760.5332-0.00640.08880.27890.00140.387918.598437.50073.6553
144.27580.826-0.59944.0887-0.33132.77130.38470.08780.28670.1685-0.1474-0.25880.2830.4152-0.12910.25990.0592-0.00190.2708-0.04190.180726.409418.32575.3991
151.7852-0.6507-0.1762.56550.47821.85820.1414-0.0874-0.2392-0.21830.1413-0.1096-0.06090.1404-0.23010.24070.00630.00290.3543-0.01270.334123.097620.3927-3.7596
161.4287-0.5905-0.50753.51992.17543.34970.18380.0613-0.0690.11190.0171-0.0290.3420.0962-0.14160.25420.0334-0.00240.2470.00080.273520.937216.12926.1061
172.29541.8024-0.78652.39340.56241.6939-0.01330.40550.0401-0.3050.0234-0.2449-0.1517-0.1170.05430.4590.00190.03380.30680.00580.219422.1683-8.6035-5.2925
181.9840.0514-0.44672.7562-1.75674.672-0.158-0.3465-0.0250.288-0.10930.2362-0.47450.14270.11340.29470.07790.03210.32960.02760.294826.3879-23.03917.3388
191.24430.6753-0.19773.0703-1.18432.7074-0.1675-0.09210.016-0.21080.07730.3239-0.2278-0.36630.06520.31980.03060.00880.3676-0.02250.325716.6793-14.89447.1702
200.6454-0.04730.33121.9147-1.26682.80930.019-0.16480.00950.04950.01470.14610.0523-0.0205-0.00430.25330.03340.02580.29770.0050.232920.1218-21.39688.3613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 2:36)H2 - 36
2X-RAY DIFFRACTION2(chain H and resid 37:49)H37 - 49
3X-RAY DIFFRACTION3(chain H and resid 50:87)H50 - 87
4X-RAY DIFFRACTION4(chain H and resid 88:99)H88 - 99
5X-RAY DIFFRACTION5(chain H and resid 100:122)H100 - 122
6X-RAY DIFFRACTION6(chain H and resid 123:132)H123 - 132
7X-RAY DIFFRACTION7(chain H and resid 133:152)H133 - 152
8X-RAY DIFFRACTION8(chain H and resid 153:209)H153 - 209
9X-RAY DIFFRACTION9(chain H and resid 210:219)H210 - 219
10X-RAY DIFFRACTION10(chain H and resid 220:227)H220 - 227
11X-RAY DIFFRACTION11(chain L and resid 1:13)L1 - 13
12X-RAY DIFFRACTION12(chain L and resid 14:27)L14 - 27
13X-RAY DIFFRACTION13(chain L and resid 28:39)L28 - 39
14X-RAY DIFFRACTION14(chain L and resid 40:58)L40 - 58
15X-RAY DIFFRACTION15(chain L and resid 59:86)L59 - 86
16X-RAY DIFFRACTION16(chain L and resid 87:113)L87 - 113
17X-RAY DIFFRACTION17(chain L and resid 114:123)L114 - 123
18X-RAY DIFFRACTION18(chain L and resid 124:143)L124 - 143
19X-RAY DIFFRACTION19(chain L and resid 144:174)L144 - 174
20X-RAY DIFFRACTION20(chain L and resid 175:221)L175 - 221

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