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- PDB-4osu: Crystal structure of HCMV gB-neutralizing SM5-1 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4osu
TitleCrystal structure of HCMV gB-neutralizing SM5-1 Fab fragment
Components
  • SM5-1 Fab Heavy Chain
  • SM5-1 Fab Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Immune response / HCMV neutralization / HCMV glycoprotein B
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDiestel, U. / Muller, Y.A.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structural basis for the recognition of human cytomegalovirus glycoprotein B by a neutralizing human antibody.
Authors: Spindler, N. / Diestel, U. / Stump, J.D. / Wiegers, A.K. / Winkler, T.H. / Sticht, H. / Mach, M. / Muller, Y.A.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: SM5-1 Fab Heavy Chain
L: SM5-1 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82911
Polymers47,4612
Non-polymers3689
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-39 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.645, 92.645, 124.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-416-

HOH

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Components

#1: Antibody SM5-1 Fab Heavy Chain


Mass: 24878.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#2: Antibody SM5-1 Fab Light Chain


Mass: 22583.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 14, 2012
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.87→46.32 Å / Num. all: 45559 / Num. obs: 43280 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5
Reflection shellResolution: 1.87→1.92 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
mxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→46.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.282 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23462 2278 5 %RANDOM
Rwork0.18916 ---
obs0.1914 43280 99.86 %-
all-45558 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 23 382 3641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9564726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24424.545121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2731511
X-RAY DIFFRACTIONr_chiral_restr0.1590.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8850.6561789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4410.9742243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6170.7721663
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.2078.3875528
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 163 -
Rwork0.229 3097 -
obs--98.31 %
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)
119.31644.79796.94542.42051.86493.55950.12240.5898-0.79210.09250.1407-0.26630.24620.3684-0.26310.07750.0676-0.00280.076-0.01340.303146.9179.86857.63
22.8890.47510.46611.21320.23141.24890.0246-0.1528-0.10950.1654-0.0133-0.08670.07870.1089-0.01130.06310.0137-0.01210.07050.02280.220339.54417.94862.915
38.5516-5.01883.652511.4881-12.346114.94420.0903-1.17790.31061.59960.42360.046-1.53360.0511-0.51390.47-0.0431-0.10220.3859-0.11210.378750.31928.5571.872
40.2751-0.28-0.25940.42050.18830.3704-0.00160.0394-0.0784-0.1042-0.088-0.07420.1436-0.04770.08960.1710.01470.03320.1299-0.00860.321133.1019.80144.469
51.5976-1.17530.18492.3168-1.50456.49240.1130.3591-0.003-0.6219-0.5785-0.60821.14720.81310.46550.31650.19630.18410.29040.0690.478131.8611.75629.21
60.82490.1856-0.31643.2253-0.528822.69040.14620.1622-0.2809-0.5138-0.3609-0.27052.55510.2310.21470.52830.12970.13050.0881-0.04090.394426.876-4.76932.663
71.2079-1.0738-0.26711.59471.15065.80660.105-0.0410.2569-0.11840.1213-0.0725-0.7468-0.0948-0.22630.12040.0140.08370.0830.01530.323648.37936.22947.226
81.09250.0812-0.14471.49070.64622.82660.03050.01820.07950.01930.1216-0.1372-0.04830.139-0.15210.01570.01980.03480.0945-0.01340.253254.31428.73448.06
90.826-0.7339-2.46840.83182.74119.1180.03030.01570.0548-0.0374-0.02130.0092-0.1281-0.1755-0.0090.09480.03460.02960.13810.01570.299945.57828.95143.561
1011.4629.0777-0.46768.52140.74131.4826-0.00440.50770.410.01550.03410.41230.0425-0.135-0.02970.03010.01510.00990.1941-0.03020.278626.49715.44123.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 10
2X-RAY DIFFRACTION2H11 - 101
3X-RAY DIFFRACTION3H102 - 116
4X-RAY DIFFRACTION4H117 - 145
5X-RAY DIFFRACTION5H152 - 216
6X-RAY DIFFRACTION6H217 - 232
7X-RAY DIFFRACTION7L1 - 33
8X-RAY DIFFRACTION8L34 - 93
9X-RAY DIFFRACTION9L94 - 113
10X-RAY DIFFRACTION10L114 - 212

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