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- PDB-4at6: Fab fragment of antiporphyrin antibody 14H7 -

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Basic information

Entry
Database: PDB / ID: 4at6
TitleFab fragment of antiporphyrin antibody 14H7
Components
  • FAB 14H7 HEAVY CHAIN
  • FAB 14H7 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / METALLOPORPHYRIN / CATALYTIC ANTIBODY / PEROXIDASE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.549 Å
AuthorsGolinelli-Pimpaneau, B. / Mahy, J.P.
Citation
Journal: Plos One / Year: 2012
Title: Crystal Structure of Two Anti-Porphyrin Antibodies with Peroxidase Activity.
Authors: Munoz Robles, V. / Marechal, J. / Bahloul, A. / Sari, M. / Mahy, J. / Golinelli-Pimpaneau, B.
#1: Journal: FEBS Lett. / Year: 1996
Title: Artificial Peroxidase-Like Hemoproteins Based on Antibodies Constructed from a Specifically Designed Ortho-Carboxy Substituted Tetraarylporphyrin Hapten and Exhibiting a High Affinity for Iron-Porphyrins.
Authors: Quilez, R. / De Lauzon, S. / Desfosses, B. / Mansuy, D. / Mahy, J.P.
#2: Journal: FEBS Lett. / Year: 1999
Title: Studies of the Reactivity of Artificial Peroxidase-Like Hemoproteins Based on Antibodies Elicited Against a Specifically Designed Ortho-Carboxy Substituted Tetraarylporphyrin.
Authors: De Lauzon, S. / Desfosses, B. / Mansuy, D. / Mahy, J.P.
History
DepositionMay 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Sep 23, 2015Group: Data collection
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB 14H7 HEAVY CHAIN
B: FAB 14H7 LIGHT CHAIN
C: FAB 14H7 HEAVY CHAIN
D: FAB 14H7 LIGHT CHAIN
E: FAB 14H7 HEAVY CHAIN
F: FAB 14H7 LIGHT CHAIN
G: FAB 14H7 HEAVY CHAIN
H: FAB 14H7 HEAVY CHAIN
I: FAB 14H7 LIGHT CHAIN
J: FAB 14H7 HEAVY CHAIN
K: FAB 14H7 LIGHT CHAIN
L: FAB 14H7 LIGHT CHAIN
M: FAB 14H7 HEAVY CHAIN
N: FAB 14H7 LIGHT CHAIN
O: FAB 14H7 HEAVY CHAIN
P: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)365,08616
Polymers365,08616
Non-polymers00
Water6,467359
1
A: FAB 14H7 HEAVY CHAIN
B: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-23.7 kcal/mol
Surface area19890 Å2
MethodPISA
2
C: FAB 14H7 HEAVY CHAIN
D: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-24.8 kcal/mol
Surface area19990 Å2
MethodPISA
3
E: FAB 14H7 HEAVY CHAIN
F: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-23.2 kcal/mol
Surface area20140 Å2
MethodPISA
4
G: FAB 14H7 HEAVY CHAIN
I: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-27.2 kcal/mol
Surface area19740 Å2
MethodPISA
5
H: FAB 14H7 HEAVY CHAIN
L: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-23.8 kcal/mol
Surface area20020 Å2
MethodPISA
6
J: FAB 14H7 HEAVY CHAIN
K: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-25.7 kcal/mol
Surface area19650 Å2
MethodPISA
7
M: FAB 14H7 HEAVY CHAIN
N: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25.4 kcal/mol
Surface area19690 Å2
MethodPISA
8
O: FAB 14H7 HEAVY CHAIN
P: FAB 14H7 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23.5 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.203, 228.160, 146.585
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99998, 0.00174, 0.00552), (-0.00179, 0.99995, 0.01013), (-0.00551, -0.01014, 0.9999)-28.6368, -114.8162, -71.16735
2given(-0.99993, -0.0043, 0.01109), (0.00429, -0.99999, -0.00057), (0.01109, -0.00053, 0.99994)56.924, 221.69186, -0.45605
3given(-0.99999, 0.00149, 0.00429), (-0.00143, -0.99989, 0.01451), (0.00431, 0.01451, 0.99989)83.29621, 334.41403, -77.6745
4given(0.99999, 0.00013, -0.00459), (6.0E-5, -0.9999, -0.01438), (-0.00459, 0.01437, -0.99989)6.29364, 223.56726, 143.73276
5given(0.99996, -0.00197, -0.00828), (-0.00197, -1, 0.00102), (-0.00828, -0.00101, -0.99997)-19.86416, 334.85321, 219.99602
6given(-0.99951, 0.00597, -0.03067), (0.00566, 0.99993, 0.01011), (0.03073, 0.00993, -0.99948)52.7506, -229.38753, 143.23685
7given(-0.99959, 0.00346, -0.02849), (0.00287, 0.99978, 0.02069), (0.02855, 0.0206, -0.99938)82.67383, -345.29367, 210.2587
8given(0.99999, -0.00165, -0.00463), (0.0017, 0.99995, 0.00973), (0.00462, -0.00974, 0.99994)-27.14069, -114.91891, -71.53188
9given(-0.99998, -0.00152, 0.00656), (0.00158, -0.99995, 0.01027), (0.00654, 0.01028, 0.99993)56.35285, 221.65279, -2.13283
10given(-0.99983, 0.01367, -0.01252), (-0.01378, -0.99986, 0.00947), (-0.01239, 0.00964, 0.99988)80.95904, 335.77966, -74.75822
11given(0.99937, 0.02064, 0.02897), (0.02021, -0.99968, 0.01518), (0.02927, -0.01459, -0.99946)-2.13621, 219.69167, 149.46565
12given(0.99945, 0.02054, 0.0261), (0.01953, -0.99907, 0.03836), (0.02687, -0.03783, -0.99892)-33.92951, 326.4978, 230.21596
13given(-0.99958, 0.01141, -0.02661), (0.01225, 0.99942, -0.03168), (0.02623, -0.03199, -0.99914)51.12217, -224.4111, 154.2587
14given(-0.99965, 0.00573, -0.02585), (0.00627, 0.99976, -0.02085), (0.02573, -0.02101, -0.99945)81.5119, -337.38531, 226.04016

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Components

#1: Antibody
FAB 14H7 HEAVY CHAIN


Mass: 22912.578 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#2: Antibody
FAB 14H7 LIGHT CHAIN


Mass: 22723.164 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growpH: 6.5
Details: 25% PEG 4000, 0.1 M AMMONIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.499
ReflectionResolution: 2.55→20 Å / Num. obs: 112207 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 1.19 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.36
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.17 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.09 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MFA AND 1MF

1mfa


Resolution: 2.549→16.652 Å / σ(F): 1.38 / Phase error: 40.46 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUES H1-H6, A1-A5, C1-C8, E1-E8, G1-G5, J1-J5, M1-M7, O1-O7, G23-G29, J24-J28, M23-M29, O23-28 THAT ARE DISORDERED WERE NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.3281 5292 4.7 %
Rwork0.2791 --
obs0.2813 111576 93.45 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.775 Å2 / ksol: 0.487 e/Å3
Displacement parametersBiso mean: 46.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.7717 Å20 Å21.9074 Å2
2---0.4619 Å20 Å2
3---9.2336 Å2
Refinement stepCycle: LAST / Resolution: 2.549→16.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24879 0 0 359 25238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325526
X-RAY DIFFRACTIONf_angle_d0.74734932
X-RAY DIFFRACTIONf_dihedral_angle_d10.9038803
X-RAY DIFFRACTIONf_chiral_restr0.054115
X-RAY DIFFRACTIONf_plane_restr0.0054433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5677-2.61050.34312350.31574671X-RAY DIFFRACTION84
2.6105-2.65640.34562400.30764863X-RAY DIFFRACTION85
2.6564-2.70560.36452330.31934789X-RAY DIFFRACTION85
2.7056-2.75870.37532410.31844816X-RAY DIFFRACTION85
2.7587-2.81630.37332480.30254950X-RAY DIFFRACTION87
2.8163-2.8790.36472510.30324887X-RAY DIFFRACTION87
2.879-2.94760.32622490.29545038X-RAY DIFFRACTION88
2.9476-3.02330.31772520.2945010X-RAY DIFFRACTION89
3.0233-3.10740.382560.28935091X-RAY DIFFRACTION90
3.1074-3.20180.3552500.28925022X-RAY DIFFRACTION89
3.2018-3.30880.29292600.28055223X-RAY DIFFRACTION91
3.3088-3.43160.30582540.27665126X-RAY DIFFRACTION91
3.4316-3.5750.31172530.27235227X-RAY DIFFRACTION92
3.575-3.74590.34582530.25825300X-RAY DIFFRACTION93
3.7459-3.9550.30862610.24815255X-RAY DIFFRACTION93
3.955-4.22020.29822600.23745299X-RAY DIFFRACTION94
4.2202-4.57480.29732600.22835328X-RAY DIFFRACTION93
4.5748-5.08990.30212510.2335343X-RAY DIFFRACTION93
5.0899-5.960.34922540.25155285X-RAY DIFFRACTION94
5.96-8.12690.36372480.29375375X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 39.2178 Å / Origin y: 224.0761 Å / Origin z: 109.6263 Å
111213212223313233
T0.255 Å20.0355 Å2-0.0345 Å2-0.3288 Å2-0.0015 Å2--0.2505 Å2
L0.0089 °20.0181 °2-0.0001 °2-0.0239 °2-0.0168 °2---0.014 °2
S-0.0237 Å °0.0029 Å °0.0162 Å °0.0188 Å °0.0451 Å °0.0329 Å °-0.0079 Å °0.0003 Å °-0.0172 Å °
Refinement TLS groupSelection details: ALL

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