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- PDB-6pzh: Crystal structure of human NA-22 Fab -

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Basic information

Entry
Database: PDB / ID: 6pzh
TitleCrystal structure of human NA-22 Fab
Components
  • NA-22 Fab heavy chain
  • NA-22 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: 2.3 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-22 Fab light chain
H: NA-22 Fab heavy chain
A: NA-22 Fab light chain
B: NA-22 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)96,4154
Polymers96,4154
Non-polymers00
Water6,143341
1
L: NA-22 Fab light chain
H: NA-22 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,2082
Polymers48,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area19300 Å2
MethodPISA
2
A: NA-22 Fab light chain
B: NA-22 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,2082
Polymers48,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)72.269, 74.542, 178.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody NA-22 Fab light chain


Mass: 22890.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody NA-22 Fab heavy chain


Mass: 25317.467 Da / Num. of mol.: 2
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.: 341 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 40% ethanol, 0.02% magnium chloride

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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: 2.3→44.8 Å / Num. obs: 43271 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rpim(I) all: 0.04 / Rsym value: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2184 / CC1/2: 0.83 / Rpim(I) all: 0.25 / Rsym value: 0.48

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C2B, 4V1D
Resolution: 2.3→44.8 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.01
RfactorNum. reflection% reflection
Rfree0.2364 2171 5.02 %
Rwork0.1931 --
Obs0.1952 43207 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 0 341 6872
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056695
X-RAY DIFFRACTIONf_angle_d0.7879132
X-RAY DIFFRACTIONf_dihedral_angle_d4.5813966
X-RAY DIFFRACTIONf_chiral_restr0.0571040
X-RAY DIFFRACTIONf_plane_restr0.0051163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.2948-2.34470.30621100.26942168X-RAY DIFFRACTION84
2.3447-2.39920.28561340.23332576X-RAY DIFFRACTION100
2.3992-2.45920.30331370.232528X-RAY DIFFRACTION100
2.4592-2.52570.28921680.22712517X-RAY DIFFRACTION99
2.5257-2.60.29761370.2282538X-RAY DIFFRACTION98
2.6-2.68390.29861380.23242550X-RAY DIFFRACTION100
2.6839-2.77980.35761390.22782581X-RAY DIFFRACTION100
2.7798-2.89110.30551420.22262587X-RAY DIFFRACTION100
2.8911-3.02260.24451200.22542601X-RAY DIFFRACTION100
3.0226-3.1820.29841340.22582549X-RAY DIFFRACTION99
3.182-3.38120.23941360.21672619X-RAY DIFFRACTION100
3.3812-3.64220.25121390.19642580X-RAY DIFFRACTION100
3.6422-4.00850.20871210.19592617X-RAY DIFFRACTION99
4.0085-4.58810.1781320.15272625X-RAY DIFFRACTION99
4.5881-5.77860.16471330.14722667X-RAY DIFFRACTION99
5.7786-44.85080.20831510.16772733X-RAY DIFFRACTION98
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)
13.1527-1.54520.9061.0688-1.22510.65640.16580.5220.03120.1243-0.1805-0.15170.08060.20250.00080.2930.0394-0.01320.3601-0.02480.2874-1.156711.9303-9.3442
21.64370.8032-0.26721.097-0.5650.2169-0.1568-0.0221-0.0950.00730.02250.10340.1213-0.30610.00010.3902-0.04580.02720.3938-0.05340.3361-10.7969-14.4412-4.0859
31.1776-0.1681-0.73250.6977-0.51650.775-0.31950.7042-0.0695-0.13110.25110.12920.21050.0526-0.00010.4597-0.0720.00280.5193-0.08810.4149-10.0016-20.142-10.0652
41.18090.018-0.03872.0775-1.52150.83360.1690.1374-0.1317-0.118-0.1246-0.0010.0789-0.03480.00090.30120.0297-0.04460.3324-0.00870.2897-22.070615.642-14.6718
52.36680.9239-0.44961.12310.60570.9931-0.1572-0.18440.0642-0.03960.16920.1745-0.04890.349700.4058-0.00110.00040.5511-0.04960.4063-22.4958-17.97754.7065
62.0540.8609-1.79931.8822-1.16531.4566-0.1159-0.1208-0.2178-0.26680.07060.01560.1794-0.02890.00020.3606-0.02390.01470.25840.04970.33-5.9449-15.7736.272
71.5004-0.6497-0.5492.2770.2910.45910.11590.01810.0257-0.4568-0.15210.01720.0039-0.19580.00010.40520.0328-0.02750.36270.05240.3797-34.9523-6.874838.6198
82.24980.4854-1.13411.6317-0.78632.0469-0.05160.10350.094-0.14650.2120.2134-0.0252-0.08130.00230.3124-0.0313-0.00180.26860.0480.2593-2.88525.599727.83
90.62740.4821-0.57390.825-0.76581.25150.0850.11510.2113-0.16660.0186-0.00570.06880.05230.08270.35-0.02380.02550.30530.06620.3898-4.41582.031332.5148
102.865-2.25140.84261.6597-0.69370.9632-0.08-0.10420.22250.2957-0.0228-0.24520.08610.0632-0.00040.372-0.0206-0.0170.34180.02330.4082-35.26266.064948.5567
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 3 through 106A)
2X-RAY DIFFRACTION2chain 'L' and (resid 107 through 172 )
3X-RAY DIFFRACTION3chain 'L' and (resid 173 through 214 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 119 )
5X-RAY DIFFRACTION5chain 'H' and (resid 120 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 106A)
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 87 )
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 119 )
10X-RAY DIFFRACTION10chain 'B' and (resid 120 through 230 )

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