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- PDB-5a16: Crystal structure of Fab4201 raised against Human Erythrocyte Ani... -

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Basic information

Entry
Database: PDB / ID: 5a16
TitleCrystal structure of Fab4201 raised against Human Erythrocyte Anion Exchanger 1
Components(FAB4201 HEAVY CHAIN) x 2
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ANION EXCHANGER
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fab4201 heavy chain / Fab4201 heavy chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsArakawa, T. / Kobayashi-Yugiri, T. / Alguel, Y. / Weyand, S. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. ...Arakawa, T. / Kobayashi-Yugiri, T. / Alguel, Y. / Weyand, S. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A. / Kobayashi, T. / Hamasaki, N. / Iwata, S.
CitationJournal: Science / Year: 2015
Title: Crystal Structure of the Anion Exchanger Domain of Human Erythrocyte Band 3
Authors: Arakawa, T. / Kobayashi-Yugiri, T. / Alguel, Y. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A. / ...Authors: Arakawa, T. / Kobayashi-Yugiri, T. / Alguel, Y. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A. / Kobayashi, T. / Hamasaki, N. / Iwata, S.
History
DepositionApr 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB4201 HEAVY CHAIN
B: FAB4201 HEAVY CHAIN
C: FAB4201 HEAVY CHAIN
D: FAB4201 HEAVY CHAIN
E: FAB4201 HEAVY CHAIN
F: FAB4201 HEAVY CHAIN
G: FAB4201 HEAVY CHAIN
H: FAB4201 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)197,6208
Polymers197,6208
Non-polymers00
Water9,962553
1
G: FAB4201 HEAVY CHAIN
H: FAB4201 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers49,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-29.9 kcal/mol
Surface area19450 Å2
MethodPISA
2
C: FAB4201 HEAVY CHAIN
D: FAB4201 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers49,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
3
E: FAB4201 HEAVY CHAIN
F: FAB4201 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers49,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-29.1 kcal/mol
Surface area19390 Å2
MethodPISA
4
A: FAB4201 HEAVY CHAIN
B: FAB4201 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers49,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-29 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.190, 82.190, 270.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.99008, -0.02333, -0.13852), (0.00744, 0.99344, -0.11415), (0.14028, 0.11199, 0.98376)-35.87541, -45.42252, -5.36349
2given(0.99008, -0.02333, -0.13852), (0.00744, 0.99344, -0.11415), (0.14028, 0.11199, 0.98376)-35.87541, -45.42252, -5.36349
3given(-0.20867, 0.97797, -0.00495), (0.9705, 0.20645, -0.12454), (-0.12077, -0.03079, -0.9922)-40.78191, -5.52463, -23.13163
4given(0.99725, -0.04136, 0.06143), (0.05041, 0.98678, -0.15401), (-0.05425, 0.15669, 0.98616)-29.50855, -46.6831, -6.64579
5given(-0.99774, 0.04606, -0.04886), (0.04836, 0.99773, -0.04696), (0.04658, -0.04922, -0.9977)-50.08287, -3.02557, -65.06377
6given(-0.17527, 0.98404, -0.03074), (0.98446, 0.17551, 0.00513), (0.01044, -0.02936, -0.99951)-42.32332, -0.44566, -23.80436
7given(0.98755, -0.03314, -0.15376), (0.01462, 0.99266, -0.12005), (0.15661, 0.11631, 0.98079)-35.50687, -45.53347, -5.39392
8given(-0.99567, 0.00937, 0.09246), (0.00787, 0.99983, -0.0166), (-0.0926, -0.0158, -0.99558)-44.88203, -1.56163, -66.26737
9given(-0.19059, 0.98156, 0.01483), (0.97031, 0.19066, -0.14883), (-0.14891, -0.01398, -0.98875)-40.83091, -4.92129, -23.91949
10given(0.99689, -0.07366, 0.02813), (0.07664, 0.98906, -0.12603), (-0.01854, 0.12779, 0.99163)-29.80457, -45.58498, -5.91013
11given(-0.99837, 0.05053, -0.02641), (0.05123, 0.99834, -0.02621), (0.02504, -0.02752, -0.99931)-49.21154, -2.08371, -65.54547
12given(-0.15324, 0.98813, -0.01041), (0.98815, 0.15313, -0.01053), (-0.00881, -0.0119, -0.99989)-41.68166, -0.37004, -23.91454

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Components

#1: Antibody
FAB4201 HEAVY CHAIN


Mass: 25296.443 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: GP64 TRANSGENIC MICE / References: UniProt: A0A0M3KL48*PLUS
#2: Antibody
FAB4201 HEAVY CHAIN


Mass: 24108.564 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: GP64 TRANSGENIC MICE / References: UniProt: A0A0M3KL49*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 12% (W/V) PEG20000, 0.1% NA ACETATE (PH5.3)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→82 Å / Num. obs: 61639 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R8S

2r8s


Resolution: 2.5→39.514 Å / SU ML: 0.39 / σ(F): 1.57 / Phase error: 26.61 / Stereochemistry target values: ML
Details: THE LAST 10 RESIDUES OF THE HEAVY CHAIN ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2552 6165 5.1 %
Rwork0.2128 --
obs0.2149 121946 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13608 0 0 553 14161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413988
X-RAY DIFFRACTIONf_angle_d0.93319104
X-RAY DIFFRACTIONf_dihedral_angle_d14.1914980
X-RAY DIFFRACTIONf_chiral_restr0.0392136
X-RAY DIFFRACTIONf_plane_restr0.0042412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.36756650.316411581X-RAY DIFFRACTION100
2.5894-2.6930.34645900.293311642X-RAY DIFFRACTION100
2.693-2.81560.32836360.276211640X-RAY DIFFRACTION100
2.8156-2.9640.29876020.258411592X-RAY DIFFRACTION100
2.964-3.14960.28086390.24911595X-RAY DIFFRACTION100
3.1496-3.39260.27936210.227311632X-RAY DIFFRACTION100
3.3926-3.73380.26126180.208211629X-RAY DIFFRACTION100
3.7338-4.27360.22215720.18511585X-RAY DIFFRACTION100
4.2736-5.38210.17565840.145411519X-RAY DIFFRACTION99
5.3821-39.51870.20116380.165311366X-RAY DIFFRACTION98
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)
12.69050.239-0.66872.32790.46482.378-0.17620.04640.0556-0.19480.1343-0.04660.05890.06080.07930.3614-0.00950.01780.1364-0.01580.1636-3.54953.669-6.8635
22.97020.4344-2.73442.9764-2.56964.330.49820.26480.14570.3660.10820.3237-1.0876-0.7809-0.13820.63650.1130.16750.38620.03290.2096-1.523146.3039-40.2084
32.76050.4654-0.75382.826-0.49723.3988-0.0598-0.3120.07680.1630.03840.0526-0.1246-0.35450.06210.13260.0182-0.04940.2868-0.0330.1323-39.69918.6482-6.5999
42.5858-0.0140.42331.6682-0.60724.5036-0.07410.2536-0.04890.0046-0.0423-0.081-0.0734-0.16240.1060.08680.00060.01540.236-0.02020.2088-35.40495.1292-38.9687
54.25310.2131-2.1192.88010.44063.8340.05470.04910.19730.42640.044-0.0057-0.0727-0.0906-0.08710.42720.0715-0.04210.22920.00050.1752-41.073552.1185-59.9784
62.6573-0.5347-0.61871.3353-0.15173.52510.467-0.09150.2679-0.37850.1505-0.3096-0.40810.1124-0.18520.7131-0.15370.24410.2232-0.03420.2106-44.476644.9938-27.2971
72.27490.55210.85633.45721.10374.86940.11630.2147-0.0014-0.05210.0516-0.23120.04550.4527-0.13210.10720.03090.0180.18750.01530.128712.48032.9611-17.548
81.8389-0.07090.33522.0316-0.65414.3033-0.03-0.1030.11070.2220.0343-0.013-0.12470.1231-0.01550.2115-0.00050.02070.0676-0.0370.16424.75035.984415.0124
90.87830.1045-0.7422.61480.58063.1472-0.22560.1321-0.2137-0.15070.0468-0.05650.0694-0.25940.13650.4103-0.01550.07890.119-0.01360.2348-4.793631.9429-6.3233
102.30241.4956-2.0862.2682-1.22095.9027-0.2971-0.3983-0.4556-0.3625-0.3297-0.16040.76930.93780.54950.54380.14140.02820.46390.09690.25269.004635.0317-40.966
112.20911.0127-0.69492.65010.64313.4934-0.2038-0.102-0.28190.0393-0.0403-0.16630.7919-0.32180.18390.3749-0.06890.06180.220.03580.3069-40.3245-13.1348-8.6296
123.40230.7866-1.9543.475-0.52764.047-0.28350.2227-0.2087-0.11280.0981-0.07130.39940.15620.14760.1288-0.0258-0.01970.2615-0.03350.1797-24.5482-5.097-42.2306
131.2307-0.5803-0.32393.3364-1.51162.3657-0.14440.0774-0.24320.37230.0879-0.0765-0.083-0.01950.0730.32960.0811-0.04550.2508-0.06160.2336-40.406430.4369-60.0404
142.5578-1.5551-0.9982.6451.47111.86880.1301-0.0318-0.0704-0.2824-0.05160.0897-0.1412-0.3654-0.03710.4195-0.059-0.0580.31110.01070.1562-55.357834.418-25.3545
152.49130.5385-1.46730.6824-0.3324.9210.11670.26280.00350.0189-0.01210.07380.1495-0.263-0.08990.13870.0567-0.01570.13220.00440.1485-8.6666-2.5542-17.3997
162.18941.30651.44932.87782.01153.27490.0776-0.09070.23660.0838-0.12430.2122-0.4519-0.29560.0830.33940.03120.07040.0750.04060.1663-8.025814.332516.5438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESI 1:124
2X-RAY DIFFRACTION2CHAIN A AND RESI 125:226
3X-RAY DIFFRACTION3CHAIN C AND RESI 1:124
4X-RAY DIFFRACTION4CHAIN C AND RESI 125:226
5X-RAY DIFFRACTION5CHAIN E AND RESI 1:124
6X-RAY DIFFRACTION6CHAIN E AND RESI 125:226
7X-RAY DIFFRACTION7CHAIN G AND RESI 1:124
8X-RAY DIFFRACTION8CHAIN G AND RESI 125:226
9X-RAY DIFFRACTION9CHAIN B AND RESI 1:112
10X-RAY DIFFRACTION10CHAIN B AND RESI 113:218
11X-RAY DIFFRACTION11CHAIN D AND RESI 1:112
12X-RAY DIFFRACTION12CHAIN D AND RESI 113:218
13X-RAY DIFFRACTION13CHAIN F AND RESI 1:112
14X-RAY DIFFRACTION14CHAIN F AND RESI 113:218
15X-RAY DIFFRACTION15CHAIN H AND RESI 1:112
16X-RAY DIFFRACTION16CHAIN H AND RESI 113:218

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