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- PDB-4rzc: Fv M6P-1 in complex with mannose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 4rzc
TitleFv M6P-1 in complex with mannose-6-phosphate
Components
  • Fv M6P-1 heavy chain
  • Fv M6P-1 light chain
KeywordsIMMUNE SYSTEM / Antibody variable fragment / mannose-6-phosphate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 6-O-phosphono-alpha-D-mannopyranose
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.723 Å
AuthorsBlackler, R.J. / Evans, D.W. / Evans, S.V. / Muller-Loennies, S.
CitationJournal: Glycobiology / Year: 2016
Title: Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide-specific binding pocket that distinguishes N-glycan phosphorylation in a branch-specific manner.
Authors: Blackler, R.J. / Evans, D.W. / Smith, D.F. / Cummings, R.D. / Brooks, C.L. / Braulke, T. / Liu, X. / Evans, S.V. / Muller-Loennies, S.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fv M6P-1 light chain
L: Fv M6P-1 heavy chain
A: Fv M6P-1 light chain
B: Fv M6P-1 heavy chain
C: Fv M6P-1 light chain
D: Fv M6P-1 heavy chain
E: Fv M6P-1 light chain
F: Fv M6P-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,53918
Polymers98,9228
Non-polymers1,61710
Water2,756153
1
H: Fv M6P-1 light chain
L: Fv M6P-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0874
Polymers24,7302
Non-polymers3562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-21 kcal/mol
Surface area10600 Å2
MethodPISA
2
A: Fv M6P-1 light chain
B: Fv M6P-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0874
Polymers24,7302
Non-polymers3562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-21 kcal/mol
Surface area10590 Å2
MethodPISA
3
C: Fv M6P-1 light chain
D: Fv M6P-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1835
Polymers24,7302
Non-polymers4523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-31 kcal/mol
Surface area10480 Å2
MethodPISA
4
E: Fv M6P-1 light chain
F: Fv M6P-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1835
Polymers24,7302
Non-polymers4523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-31 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.607, 128.050, 127.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
12H
22C
13H
23E
14L
24B
15L
25D
16L
26F
17A
27C
18A
28E
19B
29D
110B
210F
111C
211E
112D
212F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010H0 - 116
2010A0 - 116
1020H1 - 116
2020C1 - 116
1030H1 - 116
2030E1 - 116
1040L2 - 113
2040B2 - 113
1050L2 - 113
2050D2 - 113
1060L2 - 113
2060F2 - 113
1070A1 - 116
2070C1 - 116
1080A1 - 116
2080E1 - 116
1090B2 - 113
2090D2 - 113
10100B2 - 113
20100F2 - 113
10110C1 - 117
20110E1 - 117
10120D2 - 113
20120F2 - 113

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Antibody
Fv M6P-1 light chain


Mass: 12650.101 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pSJF8 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1
#2: Antibody
Fv M6P-1 heavy chain


Mass: 12080.325 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pSJF8 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1
#3: Sugar
ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris, Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 24, 2012
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.519
11-H, L, K20.481
ReflectionResolution: 2.7→30.09 Å / Num. obs: 21952 / % possible obs: 81.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.105 / Χ2: 1.012 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.82.50.39222991.064186.3
2.8-2.912.50.29222911.014186.3
2.91-3.042.50.20722591.036185.4
3.04-3.22.50.18122791.015185.5
3.2-3.42.50.14122800.972185
3.4-3.662.50.11318460.956169.2
3.66-4.032.50.10219630.951172.8
4.03-4.612.60.06122541.037183
4.61-5.82.60.05522371.002181.5
5.8-302.60.05322441.053177.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.723→30.09 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.215 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1094 5 %RANDOM
Rwork0.2261 ---
obs0.2283 21952 80.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.15 Å2 / Biso mean: 30.376 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---4.1 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.723→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6879 0 94 153 7126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027129
X-RAY DIFFRACTIONr_bond_other_d0.0040.026403
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.959695
X-RAY DIFFRACTIONr_angle_other_deg1.155314760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39623.481270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.634151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7411532
X-RAY DIFFRACTIONr_chiral_restr0.090.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028020
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021656
X-RAY DIFFRACTIONr_mcbond_it0.6841.5983634
X-RAY DIFFRACTIONr_mcbond_other0.6841.5983633
X-RAY DIFFRACTIONr_mcangle_it1.2132.3924518
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H61040.1
12A61040.1
21H59370.12
22C59370.12
31H59980.1
32E59980.1
41L53730.12
42B53730.12
51L52650.14
52D52650.14
61L53560.13
62F53560.13
71A59060.12
72C59060.12
81A58810.12
82E58810.12
91B52180.15
92D52180.15
101B53790.14
102F53790.14
111C60520.11
112E60520.11
121D54300.13
122F54300.13
LS refinement shellResolution: 2.723→2.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 51 -
Rwork0.269 1444 -
all-1495 -
obs--75.85 %
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)
11.62210.196-0.35490.7444-0.2491.73720.0151-0.10840.0267-0.1615-0.00930.08760.0025-0.1039-0.00580.18790.0295-0.00150.1999-0.01180.1087-31.2447-9.719710.6185
20.1080.1948-0.55861.291-0.27744.16240.0116-0.057-0.04260.0132-0.0767-0.15180.16060.230.06510.0764-0.0043-0.01570.15790.00870.0995-15.8456-17.74423.2178
31.4053-0.2239-0.03090.8370.45151.828-0.138-0.0973-0.0808-0.10530.1485-0.13150.04570.1917-0.01050.11940.036-0.01020.19640.00860.08840.7327-51.282613.9446
40.15660.03760.18841.18860.36695.14780.0069-0.00430.0166-0.019-0.00830.1603-0.1861-0.28370.00140.0240.00180.00340.1109-0.00130.0409-14.4807-43.0226.9593
51.54370.9897-0.26652.67940.74310.6372-0.00950.0257-0.0654-0.0363-0.0323-0.1665-0.14750.05470.04170.174-0.0142-0.00060.2309-0.00850.147516.191-42.78444.6732
60.19340.0728-0.44793.0869-0.50721.20090.03830.1025-0.09650.1177-0.20230.3633-0.0375-0.21070.1640.0608-0.0115-0.00540.214-0.02960.13880.8013-55.271252.9085
72.4484-0.09960.16052.83430.41951.32630.0054-0.0245-0.2361-0.0655-0.1110.20430.0569-0.10130.10560.0568-0.01820.01060.1910.02890.065914.3213-18.117541.4772
81.44330.03010.21582.95210.76180.94090.0516-0.08950.1292-0.0284-0.0279-0.2809-0.01890.1129-0.02370.0506-0.0115-0.00680.2404-0.00230.099529.7707-5.317149.4197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H0 - 117
2X-RAY DIFFRACTION2L2 - 113
3X-RAY DIFFRACTION3A-1 - 117
4X-RAY DIFFRACTION4B2 - 113
5X-RAY DIFFRACTION5C1 - 117
6X-RAY DIFFRACTION6D2 - 113
7X-RAY DIFFRACTION7E1 - 117
8X-RAY DIFFRACTION8F2 - 113

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