HEADER SUGAR BINDING PROTEIN 29-MAY-23 8JIY TITLE A CARBOHYDRATE BINDING DOMAIN OF A PUTATIVE CHONDROITINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF4955 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POLARIBACTER HALIOTIS; SOURCE 3 ORGANISM_TAXID: 1888915; SOURCE 4 GENE: H9I45_07735; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CARBOHYDRATE BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.C.LIU,Y.G.CHANG REVDAT 2 03-APR-24 8JIY 1 JRNL REVDAT 1 20-SEP-23 8JIY 0 JRNL AUTH G.LIU,Y.CHANG,X.MEI,G.CHEN,Y.ZHANG,X.JIANG,W.TAO,C.XUE JRNL TITL IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF A NOVEL JRNL TITL 2 CHONDROITIN SULFATE-SPECIFIC CARBOHYDRATE-BINDING MODULE: JRNL TITL 3 THE FIRST MEMBER OF A NEW FAMILY, CBM100. JRNL REF INT.J.BIOL.MACROMOL. V. 255 27959 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 37951443 JRNL DOI 10.1016/J.IJBIOMAC.2023.127959 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 32661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.150 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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 3.7300 - 2.9600 0.99 2233 147 0.1779 0.2032 REMARK 3 2 2.9600 - 2.5900 1.00 2221 147 0.1898 0.2054 REMARK 3 3 2.5900 - 2.3500 0.99 2188 142 0.1927 0.2457 REMARK 3 4 2.3500 - 2.1800 0.98 2174 146 0.1890 0.2324 REMARK 3 5 2.1800 - 2.0600 0.99 2191 137 0.1879 0.2105 REMARK 3 6 2.0600 - 1.9500 0.99 2143 144 0.1831 0.2035 REMARK 3 7 1.9500 - 1.8700 0.99 2187 142 0.2068 0.2639 REMARK 3 8 1.8700 - 1.8000 0.99 2162 144 0.2175 0.2468 REMARK 3 9 1.8000 - 1.7300 0.99 2165 142 0.2191 0.2554 REMARK 3 10 1.7300 - 1.6800 1.00 2171 138 0.2313 0.2643 REMARK 3 11 1.6800 - 1.6300 0.99 2154 140 0.2412 0.2941 REMARK 3 12 1.6300 - 1.5900 0.99 2168 142 0.2500 0.3033 REMARK 3 13 1.5900 - 1.5500 0.99 2145 141 0.2561 0.2837 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.620 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 : 0.006 NULL REMARK 3 ANGLE : 0.767 NULL REMARK 3 CHIRALITY : 0.056 266 REMARK 3 PLANARITY : 0.005 315 REMARK 3 DIHEDRAL : 6.059 236 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 8JIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 06-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300037879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32725 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 43.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.23800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 28.15650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.72800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.31700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.72800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.15650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.31700 REMARK 290 SMTRY3 4 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 THR A 1 REMARK 465 LEU A 2 REMARK 465 THR A 3 REMARK 465 SER A 220 REMARK 465 ASN A 221 REMARK 465 THR A 222 REMARK 465 SER A 223 REMARK 465 PHE A 224 REMARK 465 ILE A 225 REMARK 465 ILE A 226 REMARK 465 GLU A 227 REMARK 465 ASP A 228 REMARK 465 THR A 229 REMARK 465 ILE A 230 REMARK 465 LYS A 231 REMARK 465 LEU A 232 REMARK 465 GLU A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 334 O HOH A 533 2.06 REMARK 500 O HOH A 533 O HOH A 566 2.09 REMARK 500 O HOH A 337 O HOH A 347 2.11 REMARK 500 O HOH A 427 O HOH A 540 2.12 REMARK 500 O HOH A 386 O HOH A 516 2.16 REMARK 500 O HOH A 519 O HOH A 536 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 TYR A 7 134.59 -39.88 REMARK 500 TYR A 12 91.87 -164.77 REMARK 500 ASN A 29 62.98 -151.74 REMARK 500 THR A 140 -58.22 -125.84 REMARK 500 ASN A 141 17.49 -153.88 REMARK 500 ASN A 200 84.67 -150.71 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8JIY A 1 231 UNP A0A7L8AJZ3_9FLAO DBREF2 8JIY A A0A7L8AJZ3 555 785 SEQADV 8JIY MET A -1 UNP A0A7L8AJZ INITIATING METHIONINE SEQADV 8JIY GLY A 0 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY LEU A 232 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY GLU A 233 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 234 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 235 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 236 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 237 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 238 UNP A0A7L8AJZ EXPRESSION TAG SEQADV 8JIY HIS A 239 UNP A0A7L8AJZ EXPRESSION TAG SEQRES 1 A 241 MET GLY THR LEU THR ASN PRO PHE TYR PRO ILE PHE TYR SEQRES 2 A 241 TYR GLU ASP PHE GLY ALA VAL ASN GLN GLY TYR SER VAL SEQRES 3 A 241 GLN ILE VAL LYS ASN THR ASN SER GLN ASN GLU ALA GLN SEQRES 4 A 241 ILE GLY LYS ARG VAL ASN ASP ILE PRO ASP ALA ALA ASP SEQRES 5 A 241 SER ASN ASN GLU PHE THR GLU ALA ARG PRO ALA ASN ARG SEQRES 6 A 241 ILE PRO ALA ASN SER ALA ARG ASN GLN LYS ALA ILE ALA SEQRES 7 A 241 ILE VAL GLY THR SER SER ASN THR ASN TYR GLU LEU GLU SEQRES 8 A 241 ALA TRP VAL THR MET PRO ILE ILE ASP VAL SER LYS ASN SEQRES 9 A 241 ASN GLN TYR ILE ASN ALA ASP ASP THR PHE LYS TYR VAL SEQRES 10 A 241 SER PHE TRP THR GLU GLN ARG TYR ALA ASN GLY GLY ILE SEQRES 11 A 241 SER SER LEU GLU VAL PHE ILE SER THR ASP TYR THR ASN SEQRES 12 A 241 ASN VAL THR THR ALA ASN TRP THR ASN VAL THR SER ASN SEQRES 13 A 241 VAL ASN LYS ILE ALA THR SER GLY GLN ASN PRO GLN THR SEQRES 14 A 241 TYR VAL GLU SER LEU LEU ASP ILE SER SER TYR THR ASP SEQRES 15 A 241 THR ASN PHE THR LEU ALA PHE LYS TYR THR SER ASP ASN SEQRES 16 A 241 SER THR TYR SER GLY SER ASN ARG ASN GLY THR PHE TYR SEQRES 17 A 241 ILE SER ASP VAL LYS TYR PHE VAL SER ASP THR THR LEU SEQRES 18 A 241 SER ASN THR SER PHE ILE ILE GLU ASP THR ILE LYS LEU SEQRES 19 A 241 GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *270(H2 O) HELIX 1 AA1 ASN A 34 ALA A 36 5 3 HELIX 2 AA2 ASP A 47 SER A 51 5 5 HELIX 3 AA3 ASN A 142 ALA A 146 5 5 HELIX 4 AA4 THR A 152 VAL A 155 5 4 SHEET 1 AA1 4 ILE A 9 TYR A 12 0 SHEET 2 AA1 4 THR A 204 SER A 215 -1 O TYR A 212 N TYR A 11 SHEET 3 AA1 4 ALA A 74 VAL A 78 -1 N ILE A 75 O ILE A 207 SHEET 4 AA1 4 ILE A 38 VAL A 42 -1 N LYS A 40 O ALA A 76 SHEET 1 AA2 4 ILE A 9 TYR A 12 0 SHEET 2 AA2 4 THR A 204 SER A 215 -1 O TYR A 212 N TYR A 11 SHEET 3 AA2 4 PHE A 112 ARG A 122 -1 N TYR A 114 O PHE A 213 SHEET 4 AA2 4 VAL A 169 ASP A 174 -1 O SER A 171 N PHE A 117 SHEET 1 AA3 5 SER A 23 ASN A 29 0 SHEET 2 AA3 5 LEU A 88 THR A 93 -1 O TRP A 91 N GLN A 25 SHEET 3 AA3 5 THR A 184 SER A 191 -1 O TYR A 189 N ALA A 90 SHEET 4 AA3 5 SER A 129 SER A 136 -1 N SER A 136 O THR A 184 SHEET 5 AA3 5 THR A 149 ASN A 150 -1 O THR A 149 N ILE A 135 SHEET 1 AA4 2 THR A 80 SER A 81 0 SHEET 2 AA4 2 THR A 84 ASN A 85 -1 O THR A 84 N SER A 81 CISPEP 1 TYR A 7 PRO A 8 0 3.91 CISPEP 2 ILE A 64 PRO A 65 0 2.81 CRYST1 56.313 56.634 69.456 90.00 90.00 90.00 P 21 21 21 4 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 0.017758 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014398 0.00000