PDB Short entry for 5BZR HEADER PROTEIN BINDING 11-JUN-15 5BZR TITLE CRYSTAL STRUCTURE OF THE MURINE CD44 HYALURONAN BINDING DOMAIN COMPLEX TITLE 2 WITH A SMALL MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD44 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HYALURONAN BINDING DOMAIN, RESIDUES 21-171; COMPND 5 SYNONYM: EXTRACELLULAR MATRIX RECEPTOR III,ECMR-III,GP90 LYMPHOCYTE COMPND 6 HOMING/ADHESION RECEPTOR,HUTCH-I,HERMES ANTIGEN,HYALURONATE RECEPTOR, COMPND 7 LYMPHOCYTE ANTIGEN 24,LY-24,PHAGOCYTIC GLYCOPROTEIN 1,PGP-1, COMPND 8 PHAGOCYTIC GLYCOPROTEIN I,PGP-I; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS LINK MODULE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.K.LIU,B.C.FINZEL REVDAT 1 29-JUN-16 5BZR 0 JRNL AUTH L.K.LIU,B.C.FINZEL JRNL TITL CRYSTAL STRUCTURE OF THE MURINE CD44 HYALURONAN BINDING JRNL TITL 2 DOMAIN COMPLEX WITH A SMALL MOLECULE JRNL REF TO BE PUBLISHED REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 45492 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2279 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1171 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.039 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.501 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5BZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-13 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 : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.856 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 5000, MES, (NH4)2SO4, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 40.85650 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 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 345 O HOH A 363 2.06 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 32 152.07 -47.51 REMARK 500 SER A 47 13.11 -156.64 REMARK 500 GLU A 131 -131.39 -118.98 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 DMS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4XM A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BZC RELATED DB: PDB REMARK 900 RELATED ID: 5BZE RELATED DB: PDB REMARK 900 RELATED ID: 5BZF RELATED DB: PDB REMARK 900 RELATED ID: 5BZG RELATED DB: PDB REMARK 900 RELATED ID: 5BZH RELATED DB: PDB REMARK 900 RELATED ID: 5BZI RELATED DB: PDB REMARK 900 RELATED ID: 5BZJ RELATED DB: PDB REMARK 900 RELATED ID: 5BZM RELATED DB: PDB REMARK 900 RELATED ID: 5BZN RELATED DB: PDB REMARK 900 RELATED ID: 5BZO RELATED DB: PDB REMARK 900 RELATED ID: 5BZQ RELATED DB: PDB REMARK 900 RELATED ID: 5BZP RELATED DB: PDB REMARK 900 RELATED ID: 5BZS RELATED DB: PDB REMARK 900 RELATED ID: 5BZT RELATED DB: PDB DBREF 5BZR A 23 173 UNP P15379 CD44_MOUSE 21 171 SEQADV 5BZR MET A 23 UNP P15379 HIS 21 ENGINEERED MUTATION SEQADV 5BZR ASN A 24 UNP P15379 GLN 22 ENGINEERED MUTATION SEQRES 1 A 151 MET ASN GLN ILE ASP LEU ASN VAL THR CYS ARG TYR ALA SEQRES 2 A 151 GLY VAL PHE HIS VAL GLU LYS ASN GLY ARG TYR SER ILE SEQRES 3 A 151 SER ARG THR GLU ALA ALA ASP LEU CYS GLN ALA PHE ASN SEQRES 4 A 151 SER THR LEU PRO THR MET ASP GLN MET LYS LEU ALA LEU SEQRES 5 A 151 SER LYS GLY PHE GLU THR CYS ARG TYR GLY PHE ILE GLU SEQRES 6 A 151 GLY ASN VAL VAL ILE PRO ARG ILE HIS PRO ASN ALA ILE SEQRES 7 A 151 CYS ALA ALA ASN HIS THR GLY VAL TYR ILE LEU VAL THR SEQRES 8 A 151 SER ASN THR SER HIS TYR ASP THR TYR CYS PHE ASN ALA SEQRES 9 A 151 SER ALA PRO PRO GLU GLU ASP CYS THR SER VAL THR ASP SEQRES 10 A 151 LEU PRO ASN SER PHE ASP GLY PRO VAL THR ILE THR ILE SEQRES 11 A 151 VAL ASN ARG ASP GLY THR ARG TYR SER LYS LYS GLY GLU SEQRES 12 A 151 TYR ARG THR HIS GLN GLU ASP ILE HET DMS A 201 4 HET 4XM A 202 21 HET GOL A 203 6 HETNAM DMS DIMETHYL SULFOXIDE HETNAM 4XM 2-[3-(TETRAHYDRO-2H-PYRAN-4-YLOXY)PROPYL]-1,2,3,4- HETNAM 2 4XM TETRAHYDROISOQUINOLIN-8-AMINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DMS C2 H6 O S FORMUL 3 4XM C17 H26 N2 O2 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *117(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 GLN A 25 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 LEU A 28 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 2.05 SSBOND 2 CYS A 57 CYS A 123 1555 1555 2.08 SSBOND 3 CYS A 81 CYS A 101 1555 1555 2.04 SITE 1 AC1 9 CYS A 32 ASN A 89 CYS A 134 THR A 135 SITE 2 AC1 9 SER A 136 ARG A 155 ASP A 156 HOH A 313 SITE 3 AC1 9 HOH A 336 SITE 1 AC2 13 ASN A 29 VAL A 30 THR A 31 GLU A 41 SITE 2 AC2 13 ASP A 68 CYS A 81 VAL A 153 ASN A 154 SITE 3 AC2 13 ARG A 155 HOH A 317 HOH A 358 HOH A 377 SITE 4 AC2 13 HOH A 404 SITE 1 AC3 7 TYR A 46 CYS A 81 ILE A 92 ILE A 100 SITE 2 AC3 7 ALA A 102 GLU A 131 HOH A 310 CRYST1 30.890 81.713 32.143 90.00 117.88 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 0.032373 0.000000 0.017128 0.00000 SCALE2 0.000000 0.012238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035197 0.00000