HEADER SUGAR BINDING PROTEIN 29-MAR-15 4Z2F TITLE SCLEROTIUM ROLFSII LECTIN VARIANT (SSR2) WITH FINE CARBOHYDRATE TITLE 2 SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN VARIANT 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SSR2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ATHELIA ROLFSII; SOURCE 3 ORGANISM_TAXID: 39291; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN, CARBOHYDRATE-BINDING SPECIFICITY, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.L.KANTSADI,V.I.PEPPA,D.D.LEONIDAS REVDAT 2 10-JAN-24 4Z2F 1 REMARK REVDAT 1 01-JUL-15 4Z2F 0 JRNL AUTH V.I.PEPPA,H.VENKAT,A.L.KANTSADI,S.R.INAMDAR,G.G.BHAT, JRNL AUTH 2 S.ELIGAR,A.SHIVANAND,V.B.CHACHADI,G.J.SATISHA,B.M.SWAMY, JRNL AUTH 3 V.T.SKAMNAKI,S.E.ZOGRAPHOS,D.D.LEONIDAS JRNL TITL MOLECULAR CLONING, CARBOHYDRATE SPECIFICITY AND THE CRYSTAL JRNL TITL 2 STRUCTURE OF TWO SCLEROTIUM ROLFSII LECTIN VARIANTS. JRNL REF MOLECULES V. 20 10848 2015 JRNL REFN ESSN 1420-3049 JRNL PMID 26076107 JRNL DOI 10.3390/MOLECULES200610848 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11613 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 13.5745 - 3.9441 1.00 2877 148 0.1603 0.2297 REMARK 3 2 3.9441 - 3.1434 1.00 2752 140 0.1704 0.2198 REMARK 3 3 3.1434 - 2.7498 1.00 2731 137 0.1892 0.2801 REMARK 3 4 2.7498 - 2.5001 1.00 2700 128 0.1917 0.2811 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 2346 REMARK 3 ANGLE : 0.552 3183 REMARK 3 CHIRALITY : 0.041 337 REMARK 3 PLANARITY : 0.002 417 REMARK 3 DIHEDRAL : 12.788 835 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 13.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2OFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% V/V MPD, PH 8.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.09200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.09200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.86700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.09200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.09200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.86700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.09200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.09200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.86700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.09200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.09200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.86700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 34 OD1 ASP B 37 7556 2.19 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 GLU A 86 71.43 -106.12 REMARK 500 SER A 97 -38.59 -146.71 REMARK 500 ASN B 81 59.64 -98.09 REMARK 500 SER B 97 -45.64 -145.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YLD RELATED DB: PDB REMARK 900 4YLD IS ANOTHER VARIANT (SSR1) OF SCLEROTIUM ROLFSII LECTIN DBREF 4Z2F A 0 141 PDB 4Z2F 4Z2F 0 141 DBREF 4Z2F B 0 141 PDB 4Z2F 4Z2F 0 141 SEQRES 1 A 142 MET VAL TYR LYS ILE THR VAL ARG VAL TYR GLN THR ASN SEQRES 2 A 142 PRO ASP ALA PHE PHE HIS PRO VAL GLU LYS THR VAL TRP SEQRES 3 A 142 LYS TYR ALA ASN GLY GLY THR TRP SER ILE THR ASP ASP SEQRES 4 A 142 GLN HIS VAL LEU THR MET GLY GLY SER GLY THR SER GLY SEQRES 5 A 142 THR LEU ARG PHE HIS ALA ASP ASN GLY GLU SER PHE THR SEQRES 6 A 142 ALA THR PHE GLY VAL HIS ASN TYR LYS ARG TRP CYS ASP SEQRES 7 A 142 ILE VAL THR ASN LEU ALA ALA ASP GLU THR GLY MET VAL SEQRES 8 A 142 ILE ASN GLN GLN TYR TYR SER GLN LYS ASN ARG GLU GLU SEQRES 9 A 142 ALA ARG GLU ARG GLN LEU SER ASN TYR GLN VAL LYS ASN SEQRES 10 A 142 ALA LYS GLY ARG ASN PHE GLN ILE VAL TYR THR GLU ALA SEQRES 11 A 142 GLU GLY ASN ASP LEU HIS ALA ASN LEU ILE ILE GLY SEQRES 1 B 142 MET VAL TYR LYS ILE THR VAL ARG VAL TYR GLN THR ASN SEQRES 2 B 142 PRO ASP ALA PHE PHE HIS PRO VAL GLU LYS THR VAL TRP SEQRES 3 B 142 LYS TYR ALA ASN GLY GLY THR TRP SER ILE THR ASP ASP SEQRES 4 B 142 GLN HIS VAL LEU THR MET GLY GLY SER GLY THR SER GLY SEQRES 5 B 142 THR LEU ARG PHE HIS ALA ASP ASN GLY GLU SER PHE THR SEQRES 6 B 142 ALA THR PHE GLY VAL HIS ASN TYR LYS ARG TRP CYS ASP SEQRES 7 B 142 ILE VAL THR ASN LEU ALA ALA ASP GLU THR GLY MET VAL SEQRES 8 B 142 ILE ASN GLN GLN TYR TYR SER GLN LYS ASN ARG GLU GLU SEQRES 9 B 142 ALA ARG GLU ARG GLN LEU SER ASN TYR GLN VAL LYS ASN SEQRES 10 B 142 ALA LYS GLY ARG ASN PHE GLN ILE VAL TYR THR GLU ALA SEQRES 11 B 142 GLU GLY ASN ASP LEU HIS ALA ASN LEU ILE ILE GLY HET MPD B 201 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *251(H2 O) HELIX 1 AA1 THR A 87 TYR A 95 1 9 HELIX 2 AA2 GLN A 98 ARG A 107 1 10 HELIX 3 AA3 THR B 87 TYR B 95 1 9 HELIX 4 AA4 GLN B 98 ARG B 107 1 10 SHEET 1 AA1 6 GLY A 31 THR A 36 0 SHEET 2 AA1 6 GLN A 39 MET A 44 -1 O VAL A 41 N SER A 34 SHEET 3 AA1 6 TYR A 2 GLN A 10 -1 N TYR A 2 O MET A 44 SHEET 4 AA1 6 ASP A 133 ILE A 140 1 O LEU A 138 N ARG A 7 SHEET 5 AA1 6 ASN A 121 GLU A 128 -1 N VAL A 125 O ASN A 137 SHEET 6 AA1 6 ASN A 111 LYS A 115 -1 N VAL A 114 O PHE A 122 SHEET 1 AA2 4 PHE A 17 VAL A 24 0 SHEET 2 AA2 4 SER A 50 ALA A 57 -1 O ARG A 54 N VAL A 20 SHEET 3 AA2 4 SER A 62 HIS A 70 -1 O ALA A 65 N LEU A 53 SHEET 4 AA2 4 LYS A 73 THR A 80 -1 O LYS A 73 N HIS A 70 SHEET 1 AA3 6 GLY B 31 THR B 36 0 SHEET 2 AA3 6 GLN B 39 MET B 44 -1 O VAL B 41 N SER B 34 SHEET 3 AA3 6 TYR B 2 GLN B 10 -1 N TYR B 2 O MET B 44 SHEET 4 AA3 6 ASP B 133 ILE B 140 1 O LEU B 138 N ARG B 7 SHEET 5 AA3 6 ASN B 121 GLU B 128 -1 N VAL B 125 O ASN B 137 SHEET 6 AA3 6 ASN B 111 LYS B 115 -1 N VAL B 114 O PHE B 122 SHEET 1 AA4 4 PHE B 17 VAL B 24 0 SHEET 2 AA4 4 SER B 50 ALA B 57 -1 O ARG B 54 N VAL B 20 SHEET 3 AA4 4 SER B 62 HIS B 70 -1 O ALA B 65 N LEU B 53 SHEET 4 AA4 4 LYS B 73 VAL B 79 -1 O LYS B 73 N HIS B 70 SITE 1 AC1 4 ASN A 111 GLN A 123 TYR B 27 ALA B 28 CRYST1 100.184 100.184 63.734 90.00 90.00 90.00 P 42 21 2 16 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 0.009982 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015690 0.00000