HEADER ANTIFREEZE PROTEIN 14-DEC-98 2AFP
TITLE THE SOLUTION STRUCTURE OF TYPE II ANTIFREEZE PROTEIN REVEALS A NEW
TITLE 2 MEMBER OF THE LECTIN FAMILY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN (SEA RAVEN TYPE II ANTIFREEZE PROTEIN);
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: SIX AMINO ACID HIS TAG WAS ADDED AT THE C-TERMINAL END
COMPND 6 TO FACILITATE RECOVERY OF THE SECRETED AFP FROM THE MEDIUM USING
COMPND 7 AFFINITY CHROMATOGRAPHY.
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HEMITRIPTERUS AMERICANUS;
SOURCE 3 ORGANISM_COMMON: SEA RAVEN;
SOURCE 4 ORGANISM_TAXID: 8094;
SOURCE 5 ORGAN: BLOOD;
SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC9-SRM-CTHT;
SOURCE 10 EXPRESSION_SYSTEM_GENE: SRAFP GENE
KEYWDS RECOMBINANT SEA RAVEN PROTEIN, SOLUTION BACKBONE FOLD, C-TYPE LECTIN,
KEYWDS 2 ANTIFREEZE PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 5
AUTHOR W.GRONWALD,M.C.LOEWEN,B.LIX,A.J.DAUGULIS,F.D.SONNICHSEN,P.L.DAVIES,
AUTHOR 2 B.D.SYKES
REVDAT 5 27-DEC-23 2AFP 1 REMARK
REVDAT 4 09-MAR-22 2AFP 1 REMARK
REVDAT 3 24-FEB-09 2AFP 1 VERSN
REVDAT 2 29-DEC-99 2AFP 4 HEADER COMPND REMARK JRNL
REVDAT 2 2 4 ATOM SOURCE SEQRES
REVDAT 1 23-DEC-98 2AFP 0
JRNL AUTH W.GRONWALD,M.C.LOEWEN,B.LIX,A.J.DAUGULIS,F.D.SONNICHSEN,
JRNL AUTH 2 P.L.DAVIES,B.D.SYKES
JRNL TITL THE SOLUTION STRUCTURE OF TYPE II ANTIFREEZE PROTEIN REVEALS
JRNL TITL 2 A NEW MEMBER OF THE LECTIN FAMILY.
JRNL REF BIOCHEMISTRY V. 37 4712 1998
JRNL REFN ISSN 0006-2960
JRNL PMID 9537986
JRNL DOI 10.1021/BI972788C
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 IN THE CURRENT STRUCTURES ONLY THE GLOBAL FOLD OF THE MOLECULE IS
REMARK 3 PRESENTED.
REMARK 3 REFINED HIGH RESOLUTION SOLUTION STRUCTURES ARE NOT AVAILABLE AT
REMARK 3 THE MOMENT.
REMARK 4
REMARK 4 2AFP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-98.
REMARK 100 THE DEPOSITION ID IS D_1000000287.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 5.6
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D-TOCSY; 2D-NOESY;
REMARK 210 3D-TOCSY-HSQC; 3D-NOESY-HSQC; 3D
REMARK 210 HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY600 AND UNITYPLUS600
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR, NMRPIPE, PIPP, X-PLOR 3.1
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5
REMARK 210 CONFORMERS, SELECTION CRITERIA : GLOBAL ENERGY AND LEAST
REMARK 210 RESTRAINT VIOLATION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK:
REMARK 210 THE STRUCTURE WAS DETERMINED USING TWO AND THREE DIMENSIONAL NMR
REMARK 210 SPECTROSCOPY
REMARK 210 ON 15N-LABELED AND ON THE NATIVE SEA RAVEN ANTIFREEZE.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-5
REMARK 470 RES CSSEQI ATOMS
REMARK 470 PHE A 129 O
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ASN A 6 -70.67 -159.85
REMARK 500 1 ASP A 16 -51.97 -136.09
REMARK 500 1 ARG A 17 -161.18 -71.06
REMARK 500 1 THR A 23 -45.36 -140.12
REMARK 500 1 TRP A 28 -56.68 -24.76
REMARK 500 1 HIS A 41 -175.47 -179.93
REMARK 500 1 ALA A 43 171.75 -55.75
REMARK 500 1 HIS A 46 -47.97 -148.11
REMARK 500 1 GLN A 48 -59.47 74.40
REMARK 500 1 ASN A 58 111.29 60.32
REMARK 500 1 ALA A 59 33.39 -167.62
REMARK 500 1 CYS A 69 29.54 -161.87
REMARK 500 1 LEU A 70 30.91 -154.61
REMARK 500 1 TRP A 77 -171.99 -64.60
REMARK 500 1 ASP A 79 35.32 -158.29
REMARK 500 1 MET A 83 -157.70 -116.05
REMARK 500 1 PHE A 85 109.58 62.29
REMARK 500 1 ARG A 86 89.41 176.63
REMARK 500 1 SER A 90 172.80 -56.94
REMARK 500 1 ASP A 94 175.10 60.04
REMARK 500 1 ASP A 95 38.39 -175.33
REMARK 500 1 THR A 105 166.01 -44.97
REMARK 500 1 ALA A 108 -32.15 94.38
REMARK 500 1 CYS A 111 166.91 65.34
REMARK 500 1 ASP A 113 118.65 -172.86
REMARK 500 1 CYS A 117 -43.61 106.19
REMARK 500 1 ALA A 119 72.14 -175.22
REMARK 500 1 SER A 120 95.89 -44.44
REMARK 500 1 LYS A 122 165.14 -46.25
REMARK 500 2 ASN A 6 125.03 63.56
REMARK 500 2 ALA A 9 -42.88 -171.17
REMARK 500 2 ALA A 25 98.73 -60.32
REMARK 500 2 TRP A 28 -56.88 -25.64
REMARK 500 2 ALA A 31 -71.63 -67.99
REMARK 500 2 HIS A 41 -174.52 -179.61
REMARK 500 2 SER A 44 -47.67 -135.76
REMARK 500 2 ILE A 45 162.72 63.59
REMARK 500 2 LEU A 57 -75.83 -114.14
REMARK 500 2 ASN A 58 -99.76 -64.78
REMARK 500 2 ALA A 59 -167.57 171.36
REMARK 500 2 ILE A 64 63.50 -157.05
REMARK 500 2 ALA A 68 84.21 -156.14
REMARK 500 2 ALA A 74 87.13 -153.25
REMARK 500 2 TRP A 75 -158.60 -171.03
REMARK 500 2 TRP A 77 -166.60 -67.79
REMARK 500 2 ASP A 79 32.41 -155.08
REMARK 500 2 MET A 83 -77.91 -54.88
REMARK 500 2 SER A 90 84.72 62.27
REMARK 500 2 THR A 91 -175.09 -60.56
REMARK 500 2 LYS A 92 -53.29 176.27
REMARK 500
REMARK 500 THIS ENTRY HAS 173 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 2 0.29 SIDE CHAIN
REMARK 500 1 ARG A 17 0.20 SIDE CHAIN
REMARK 500 1 ARG A 86 0.24 SIDE CHAIN
REMARK 500 2 ARG A 2 0.30 SIDE CHAIN
REMARK 500 2 ARG A 17 0.29 SIDE CHAIN
REMARK 500 2 ARG A 86 0.27 SIDE CHAIN
REMARK 500 3 ARG A 2 0.29 SIDE CHAIN
REMARK 500 3 ARG A 17 0.31 SIDE CHAIN
REMARK 500 3 ARG A 86 0.22 SIDE CHAIN
REMARK 500 4 ARG A 2 0.24 SIDE CHAIN
REMARK 500 4 ARG A 17 0.24 SIDE CHAIN
REMARK 500 4 ARG A 86 0.21 SIDE CHAIN
REMARK 500 5 ARG A 2 0.30 SIDE CHAIN
REMARK 500 5 ARG A 17 0.27 SIDE CHAIN
REMARK 500 5 ARG A 86 0.10 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2AFP A 1 129 UNP P05140 ANP_HEMAM 35 163
SEQRES 1 A 129 GLN ARG ALA GLY PRO ASN CYS PRO ALA GLY TRP GLN PRO
SEQRES 2 A 129 LEU GLY ASP ARG CYS ILE TYR TYR GLU THR THR ALA MET
SEQRES 3 A 129 THR TRP ALA LEU ALA GLU THR ASN CYS MET LYS LEU GLY
SEQRES 4 A 129 GLY HIS LEU ALA SER ILE HIS SER GLN GLU GLU HIS SER
SEQRES 5 A 129 PHE ILE GLN THR LEU ASN ALA GLY VAL VAL TRP ILE GLY
SEQRES 6 A 129 GLY SER ALA CYS LEU GLN ALA GLY ALA TRP THR TRP SER
SEQRES 7 A 129 ASP GLY THR PRO MET ASN PHE ARG SER TRP CYS SER THR
SEQRES 8 A 129 LYS PRO ASP ASP VAL LEU ALA ALA CYS CYS MET GLN MET
SEQRES 9 A 129 THR ALA ALA ALA ASP GLN CYS TRP ASP ASP LEU PRO CYS
SEQRES 10 A 129 PRO ALA SER HIS LYS SER VAL CYS ALA MET THR PHE
HELIX 1 H1 LEU A 30 LEU A 38 1 9
HELIX 2 H2 SER A 47 LEU A 57 1 11
SHEET 1 S1 1 ARG A 17 GLU A 22 0
SHEET 1 S2 1 SER A 123 PHE A 129 0
SHEET 1 S3 1 GLY A 39 LEU A 42 0
SHEET 1 S4 1 ALA A 74 TRP A 77 0
SHEET 1 S5 1 VAL A 61 ILE A 64 0
SHEET 1 S6 1 GLY A 66 CYS A 69 0
SHEET 1 S7 1 CYS A 100 ALA A 106 0
SHEET 1 S8 1 GLN A 110 LEU A 115 0
SHEET 1 S9 1 ALA A 25 TRP A 28 0
SSBOND 1 CYS A 7 CYS A 18 1555 1555 2.02
SSBOND 2 CYS A 35 CYS A 125 1555 1555 2.02
SSBOND 3 CYS A 69 CYS A 100 1555 1555 2.02
SSBOND 4 CYS A 89 CYS A 111 1555 1555 2.02
SSBOND 5 CYS A 101 CYS A 117 1555 1555 2.02
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
