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- PDB-2vh3: ranasmurfin -

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Basic information

Entry
Database: PDB / ID: 2vh3
Titleranasmurfin
Components(RANASMURFIN) x 2
KeywordsUNKNOWN FUNCTION / LTQ / BISLTQ
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1410 / : / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / extracellular region / metal ion binding / Mainly Alpha / Ranasmurfin
Function and homology information
Biological speciesPOLYPEDATES LEUCOMYSTAX (Java whipping frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsOke, M. / Ching, R.T. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / Bloch Junior, C. / Botting, C.H. / Walsh, M.A. / Latiff, A.A. ...Oke, M. / Ching, R.T. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / Bloch Junior, C. / Botting, C.H. / Walsh, M.A. / Latiff, A.A. / Kennedy, M.W. / Cooper, A. / Naismith, J.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Unusual Chromophore and Cross-Links in Ranasmurfin: A Blue Protein from the Foam Nests of a Tropical Frog.
Authors: Oke, M. / Ching, R.T. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Bloch Jr, C. / Botting, C.H. / Walsh, M.A. / Latiff, A.A. / Kennedy, M.W. / Cooper, A. / Naismith, J.H.
History
DepositionNov 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
A: RANASMURFIN
B: RANASMURFIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9419
Polymers25,3082
Non-polymers6347
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-101.2 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 59.670, 44.900
Angle α, β, γ (deg.)90.00, 93.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUAA66 - 10066 - 100
21LYSLYSLEULEUBB66 - 10066 - 100
12DAHDAHPROPROAA2 - 82 - 8
22DAHDAHPROPROBB2 - 82 - 8
13GLUGLUGLYGLYAA10 - 6410 - 64
23GLUGLUGLYGLYBB10 - 6410 - 64

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein RANASMURFIN / RSF-1


Mass: 12646.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM FROG NESTS
Source: (natural) POLYPEDATES LEUCOMYSTAX (Java whipping frog)
References: UniProt: P85511
#2: Protein RANASMURFIN / RSF-1


Mass: 12661.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM FROG NESTS
Source: (natural) POLYPEDATES LEUCOMYSTAX (Java whipping frog)
References: UniProt: P85511

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Non-polymers , 4 types, 191 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE CHROMOPHORE IN THIS ENTRY IS FORMED BY 4 RESIDUES ACROSS CHAINS A AND B. LYS (A30)-TY2 (A108)- ...THE CHROMOPHORE IN THIS ENTRY IS FORMED BY 4 RESIDUES ACROSS CHAINS A AND B. LYS (A30)-TY2 (A108)-TYR (B108)-LYS (B30) COORDINATED BY A ZINC MOLECULE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 44.52 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.16→44 Å / Num. obs: 65500 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 1.16→1.22 Å / Redundancy: 80 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.16→44.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.254 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE SEQUENCE IS FROM X-RAY STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3499 5.1 %RANDOM
Rwork0.214 ---
obs0.216 65500 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å2-0.73 Å2
2--1.8 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.16→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 33 184 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221883
X-RAY DIFFRACTIONr_bond_other_d0.0020.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.2932.0092544
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0063204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8945233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03225.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13115333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.994156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.2360.2498
X-RAY DIFFRACTIONr_nbd_other0.1840.21438
X-RAY DIFFRACTIONr_nbtor_refined0.190.2934
X-RAY DIFFRACTIONr_nbtor_other0.0840.2917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3331.51479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57921808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4913894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1944.5727
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A466loose positional0.825
12B466loose positional0.825
21A95loose positional0.185
22B95loose positional0.185
31A767loose positional0.455
32B767loose positional0.455
11A466loose thermal1.4710
12B466loose thermal1.4710
21A95loose thermal0.9910
22B95loose thermal0.9910
31A767loose thermal1.1610
32B767loose thermal1.1610
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 178
Rwork0.372 3650
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)
11.02640.0971-0.52090.3341-0.00951.1754-0.0231-0.0528-0.08320.00480.0189-0.00560.0359-0.08040.0042-0.02440.00190.02360.00240.0142-0.054213.13119.95145.088
20.2691-0.0626-0.30040.3668-0.13120.92270.00550.0411-0.0068-0.0123-0.0487-0.0379-0.0157-0.00750.0433-0.02290.00330.0244-0.00070.009-0.0473-2.81626.92126.478
31.00410.3190.08831.24540.45980.5732-0.0222-0.0365-0.00980.0206-0.0035-0.0464-0.0063-0.02720.0258-0.0237-0.00610.0127-0.00130.0095-0.05815.36923.89635.819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2B1 - 92
3X-RAY DIFFRACTION3A93 - 112
4X-RAY DIFFRACTION3B93 - 113
5X-RAY DIFFRACTION3A1113

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