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- PDB-6pzg: Crystal structure of human NA-80 Fab -

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Basic information

Entry
Database: PDB / ID: 6pzg
TitleCrystal structure of human NA-80 Fab
Components
  • NA-80 Fab heavy chain
  • NA-80 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / inhibition mechanism
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: NA-80 Fab light chain
H: NA-80 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,1382
Polymers48,1382
Non-polymers00
Water8,035446
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)102.770, 102.770, 80.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-534-

HOH

21H-365-

HOH

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Components

#1: Antibody NA-80 Fab light chain


Mass: 23344.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody NA-80 Fab heavy chain


Mass: 24793.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M sodium citrate, pH 5.6, 40% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.59→44.5 Å / Num. obs: 66498 / % possible obs: 99.9 % / Redundancy: 18.1 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.08 / Net I/σ(I): 58
Reflection shellResolution: 1.59→1.62 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3234 / CC1/2: 0.63 / Rpim(I) all: 0.35 / Rsym value: 0.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kmt, 5aze
Resolution: 1.59→44.5 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.2036 3374 5.08 %
Rwork0.1684 --
Obs0.1702 66460 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.59→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 446 3743
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013468
X-RAY DIFFRACTIONf_angle_d1.0614754
X-RAY DIFFRACTIONf_dihedral_angle_d11.1742111
X-RAY DIFFRACTIONf_chiral_restr0.063539
X-RAY DIFFRACTIONf_plane_restr0.007611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.5856-1.60830.32721240.27772547X-RAY DIFFRACTION96
1.6083-1.63230.29291270.24442596X-RAY DIFFRACTION100
1.6323-1.65780.25351480.22682596X-RAY DIFFRACTION100
1.6578-1.6850.25221490.21292593X-RAY DIFFRACTION100
1.685-1.7140.25251600.20472620X-RAY DIFFRACTION100
1.714-1.74520.21811360.19712592X-RAY DIFFRACTION100
1.7452-1.77870.20341170.20022614X-RAY DIFFRACTION100
1.7787-1.81510.24791480.19792604X-RAY DIFFRACTION100
1.8151-1.85450.21211450.19982610X-RAY DIFFRACTION100
1.8545-1.89770.21861340.19652623X-RAY DIFFRACTION100
1.8977-1.94510.21831530.18792608X-RAY DIFFRACTION100
1.9451-1.99770.23161570.18282596X-RAY DIFFRACTION100
1.9977-2.05650.21911400.18122631X-RAY DIFFRACTION100
2.0565-2.12290.23611440.18012610X-RAY DIFFRACTION100
2.1229-2.19870.1981340.17512615X-RAY DIFFRACTION100
2.1987-2.28680.2091200.17362682X-RAY DIFFRACTION100
2.2868-2.39080.18821440.17272595X-RAY DIFFRACTION100
2.3908-2.51690.20441470.17582650X-RAY DIFFRACTION100
2.5169-2.67460.19481530.16822627X-RAY DIFFRACTION100
2.6746-2.8810.20671490.17032628X-RAY DIFFRACTION100
2.881-3.17090.19891440.17342650X-RAY DIFFRACTION100
3.1709-3.62950.2311180.15772722X-RAY DIFFRACTION100
3.6295-4.57210.17971500.13242666X-RAY DIFFRACTION100
4.5721-44.51820.16981330.15462811X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refinement-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)
17.49265.5059-7.11614.1233-5.13167.02240.4466-0.47060.60090.3191-0.13630.2093-0.34350.3381-0.3450.2232-0.0141-0.00390.2524-0.06340.253437.0948-20.670419.6321
24.8470.7741-1.70452.9249-1.0873.0878-0.0247-0.275-0.2130.0699-0.0875-0.20860.15350.21980.08810.17690.0328-0.01770.1831-0.00070.183136.576-29.032416.4339
32.90233.743-4.31144.9832-5.70886.6313-0.1623-0.1699-0.3941-0.0993-0.1875-0.43730.17060.27130.36280.1638-0.0063-0.0020.2246-0.02910.203644.2669-9.84547.224
43.2715-0.17612.33852.21170.03133.16260.02360.36260.3228-1.26870.12760.58170.2919-0.31120.21030.4445-0.1241-0.27810.31630.14540.330723.7545.4214-9.929
57.1475-4.25880.8574.75-1.09891.5456-0.046-0.0964-0.1466-0.08340.20850.2154-0.02280.0004-0.110.1537-0.0563-0.00250.16590.02930.180431.69171.12182.4252
64.5942-2.6414-0.13736.13990.63761.0640.0155-0.0097-0.3923-0.0543-0.00180.26810.0048-0.0099-0.04230.1555-0.03680.00940.17870.03080.110831.898-3.14012.2664
75.6395-0.93081.29564.8431-0.51772.4805-0.2624-0.13570.3626-0.2350.21930.8518-0.3201-0.3-0.00230.18770.0047-0.0520.21550.03810.303722.39278.6291-0.7424
88.1169-3.34423.60895.4775-1.43094.1682-0.5288-0.0370.84160.12560.1984-0.3022-0.54850.00350.18880.1698-0.04850.0020.1858-0.00570.186434.8749.48441.6265
98.2412-5.5973-0.6394.50690.04093.98530.20590.6315-0.3189-0.2531-0.26710.30250.0440.20430.08560.1655-0.0469-0.04730.2018-0.01660.240717.8489-30.5575-1.341
103.5697-1.30270.38243.1733-0.17071.4075-0.09890.0902-0.31210.26820.01040.29420.1573-0.1580.0780.20030.00530.03950.1883-0.02480.210918.3321-36.9788.7576
115.7983-1.47351.76624.8605-1.75752.3963-0.13610.18370.18910.19540.06690.2464-0.0725-0.14650.1690.12960.00620.02080.1709-0.03040.145716.7723-27.36596.6627
121.12940.41460.40241.61680.39290.1896-0.17690.14860.0244-0.19910.14560.02690.04060.0396-0.05750.1628-0.01570.01680.2725-0.00890.157525.1759-18.4099-0.6433
134.79322.33040.06542.0633-0.78810.501-0.97541.1973-0.4194-0.92510.7552-0.1680.2195-0.0470.05320.4616-0.2380.04370.451-0.12070.213627.5168-6.8031-13.3987
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 0:25 )L0 - 25
2X-RAY DIFFRACTION2( CHAIN L AND RESID 26:101 )L26 - 101
3X-RAY DIFFRACTION3( CHAIN L AND RESID 102:113 )L102 - 113
4X-RAY DIFFRACTION4( CHAIN L AND RESID 114:128 )L114 - 128
5X-RAY DIFFRACTION5( CHAIN L AND RESID 129:150 )L129 - 150
6X-RAY DIFFRACTION6( CHAIN L AND RESID 151:174 )L151 - 174
7X-RAY DIFFRACTION7( CHAIN L AND RESID 175:197 )L175 - 197
8X-RAY DIFFRACTION8( CHAIN L AND RESID 198:213 )L198 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 1:17 )H1 - 17
10X-RAY DIFFRACTION10( CHAIN H AND RESID 18:82 )H18 - 82
11X-RAY DIFFRACTION11( CHAIN H AND RESID 83:95 )H83 - 95
12X-RAY DIFFRACTION12( CHAIN H AND RESID 96:136 )H96 - 136
13X-RAY DIFFRACTION13( CHAIN H AND RESID 137:228 )H137 - 228

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