HEADER PROTEIN BINDING 14-SEP-21 5SBL TITLE CD44 PANDDA ANALYSIS GROUP DEPOSITION -- THE HYALURONAN-BINDING DOMAIN TITLE 2 OF CD44 IN COMPLEX WITH Z126932614 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD44 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EXTRACELLULAR MATRIX RECEPTOR III,ECMR-III,GP90 LYMPHOCYTE COMPND 5 HOMING/ADHESION RECEPTOR,HUTCH-I,HERMES ANTIGEN,HYALURONATE RECEPTOR, COMPND 6 LYMPHOCYTE ANTIGEN 24,LY-24,PHAGOCYTIC GLYCOPROTEIN 1,PGP-1, COMPND 7 PHAGOCYTIC GLYCOPROTEIN I,PGP-I; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CD44, LY-24; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, KEYWDS 2 ANTIGEN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR W.J.BRADSHAW,V.L.KATIS,G.A.BEZERRA,L.KOEKEMOER,F.VON DELFT,C.BOUNTRA, AUTHOR 2 P.E.BRENNAN,O.GILEADI REVDAT 1 22-SEP-21 5SBL 0 JRNL AUTH W.J.BRADSHAW,V.L.KATIS,G.A.BEZERRA,L.KOEKEMOER,F.VON DELFT, JRNL AUTH 2 C.BOUNTRA,P.E.BRENNAN,O.GILEADI JRNL TITL CD44 PANDDA ANALYSIS GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 (20-APR-2021) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.0 REMARK 3 NUMBER OF REFLECTIONS : 31724 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1570 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 13.89 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 635 REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 609 REMARK 3 BIN R VALUE (WORKING SET) : 0.2366 REMARK 3 BIN FREE R VALUE : 0.2332 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.09 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 26 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1163 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02090 REMARK 3 B22 (A**2) : -0.22330 REMARK 3 B33 (A**2) : 0.20240 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01460 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.140 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.059 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.061 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.054 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.057 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1299 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1778 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 459 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 234 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1269 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 177 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1759 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 5.72 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.41 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SBL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1001404302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.91199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31724 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.198 REMARK 200 RESOLUTION RANGE LOW (A) : 26.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.7 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2JCP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM AMMONIUM SULPHATE, 100MM MES, REMARK 280 24% PEG 5,000 MME, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.73650 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 23 REMARK 465 ASN A 24 REMARK 465 ASP A 174 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 431 O HOH A 478 2.18 REMARK 500 O HOH A 498 O HOH A 535 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 CYS A 32 154.59 -47.43 REMARK 500 SER A 47 14.76 -150.59 REMARK 500 GLU A 131 -134.30 -120.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 550 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 551 DISTANCE = 6.24 ANGSTROMS DBREF 5SBL A 25 174 UNP P15379 CD44_MOUSE 23 172 SEQADV 5SBL MET A 23 UNP P15379 INITIATING METHIONINE SEQADV 5SBL ASN A 24 UNP P15379 EXPRESSION TAG SEQRES 1 A 152 MET ASN GLN ILE ASP LEU ASN VAL THR CYS ARG TYR ALA SEQRES 2 A 152 GLY VAL PHE HIS VAL GLU LYS ASN GLY ARG TYR SER ILE SEQRES 3 A 152 SER ARG THR GLU ALA ALA ASP LEU CYS GLN ALA PHE ASN SEQRES 4 A 152 SER THR LEU PRO THR MET ASP GLN MET LYS LEU ALA LEU SEQRES 5 A 152 SER LYS GLY PHE GLU THR CYS ARG TYR GLY PHE ILE GLU SEQRES 6 A 152 GLY ASN VAL VAL ILE PRO ARG ILE HIS PRO ASN ALA ILE SEQRES 7 A 152 CYS ALA ALA ASN HIS THR GLY VAL TYR ILE LEU VAL THR SEQRES 8 A 152 SER ASN THR SER HIS TYR ASP THR TYR CYS PHE ASN ALA SEQRES 9 A 152 SER ALA PRO PRO GLU GLU ASP CYS THR SER VAL THR ASP SEQRES 10 A 152 LEU PRO ASN SER PHE ASP GLY PRO VAL THR ILE THR ILE SEQRES 11 A 152 VAL ASN ARG ASP GLY THR ARG TYR SER LYS LYS GLY GLU SEQRES 12 A 152 TYR ARG THR HIS GLN GLU ASP ILE ASP HET T6J A 201 14 HET DMS A 202 4 HET DMS A 203 4 HET DMS A 204 4 HET EDO A 205 8 HETNAM T6J 2-[(METHYLSULFONYL)METHYL]-1H-BENZIMIDAZOLE HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 T6J C9 H10 N2 O2 S FORMUL 3 DMS 3(C2 H6 O S) FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *251(H2 O) HELIX 1 AA1 SER A 49 PHE A 60 1 12 HELIX 2 AA2 THR A 66 LYS A 76 1 11 HELIX 3 AA3 CYS A 101 HIS A 105 5 5 HELIX 4 AA4 HIS A 169 ILE A 173 5 5 SHEET 1 AA1 8 GLY A 107 ILE A 110 0 SHEET 2 AA1 8 VAL A 90 ARG A 94 -1 N ARG A 94 O GLY A 107 SHEET 3 AA1 8 GLY A 84 PHE A 85 -1 N GLY A 84 O VAL A 91 SHEET 4 AA1 8 ASP A 120 PHE A 124 1 O TYR A 122 N PHE A 85 SHEET 5 AA1 8 VAL A 37 LYS A 42 -1 N VAL A 40 O THR A 121 SHEET 6 AA1 8 ILE A 26 VAL A 30 -1 N ASN A 29 O GLU A 41 SHEET 7 AA1 8 PHE A 144 ASN A 154 1 O THR A 151 N ILE A 26 SHEET 8 AA1 8 ARG A 159 GLU A 165 -1 O TYR A 160 N ILE A 152 SHEET 1 AA2 2 ARG A 33 TYR A 34 0 SHEET 2 AA2 2 GLU A 132 ASP A 133 -1 O ASP A 133 N ARG A 33 SSBOND 1 CYS A 32 CYS A 134 1555 1555 2.04 SSBOND 2 CYS A 57 CYS A 123 1555 1555 2.04 SSBOND 3 CYS A 81 CYS A 101 1555 1555 2.02 CRYST1 30.668 81.473 31.911 90.00 117.75 90.00 P 1 21 1 2 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 0.032607 0.000000 0.017156 0.00000 SCALE2 0.000000 0.012274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035410 0.00000