HEADER CELL ADHESION 05-OCT-20 7KC3 TITLE X-RAY STRUCTURE OF LFA-1 I DOMAIN COLLECTED AT 273 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-L; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: CD11 ANTIGEN-LIKE FAMILY MEMBER A,LEUKOCYTE ADHESION COMPND 5 GLYCOPROTEIN LFA-1 ALPHA CHAIN,LFA-1A,LEUKOCYTE FUNCTION-ASSOCIATED COMPND 6 MOLECULE 1 ALPHA CHAIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ITGAL, CD11A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTEGRIN, ADHESION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR R.A.WOLDEYES,K.K.HALLENBECK,S.J.PFAFF,G.LEE,S.V.CORTEZ,M.J.KELLY, AUTHOR 2 K.AKASSOGLOU,M.R.ARKIN,J.S.FRASER REVDAT 2 18-OCT-23 7KC3 1 REMARK REVDAT 1 06-OCT-21 7KC3 0 JRNL AUTH R.A.WOLDEYES,K.K.HALLENBECK,S.J.PFAFF,G.LEE,S.V.CORTEZ, JRNL AUTH 2 M.J.KELLY,K.AKASSOGLOU,M.R.ARKIN,J.S.FRASER JRNL TITL DIVERGENT CONFORMATIONAL DYNAMICS CONTROLS ALLOSTERIC LIGAND JRNL TITL 2 ACCESSIBILITY ACROSS EVOLUTIONARILY RELATED JRNL TITL 3 I-DOMAIN-CONTAINING INTEGRINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 28133 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.490 REMARK 3 FREE R VALUE TEST SET COUNT : 1827 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 45.4200 - 4.2300 1.00 2318 156 0.1550 0.1894 REMARK 3 2 4.2300 - 3.3600 0.99 2214 154 0.1447 0.1823 REMARK 3 3 3.3600 - 2.9300 0.99 2188 154 0.1685 0.2103 REMARK 3 4 2.9300 - 2.6700 0.98 2157 146 0.1808 0.1973 REMARK 3 5 2.6600 - 2.4700 0.97 2132 151 0.1680 0.2211 REMARK 3 6 2.4700 - 2.3300 0.95 2100 134 0.1706 0.2103 REMARK 3 7 2.3300 - 2.2100 0.94 2068 146 0.1695 0.2142 REMARK 3 8 2.2100 - 2.1200 0.94 2069 139 0.1869 0.2298 REMARK 3 9 2.1200 - 2.0300 0.91 1979 140 0.1969 0.2520 REMARK 3 10 2.0300 - 1.9600 0.88 1917 138 0.2184 0.2341 REMARK 3 11 1.9600 - 1.9000 0.85 1844 131 0.2391 0.2835 REMARK 3 12 1.9000 - 1.8500 0.79 1716 123 0.2878 0.3311 REMARK 3 13 1.8500 - 1.8000 0.74 1604 115 0.3446 0.3315 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.902 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.07 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 : 0.010 1540 REMARK 3 ANGLE : 1.069 2070 REMARK 3 CHIRALITY : 0.058 234 REMARK 3 PLANARITY : 0.007 261 REMARK 3 DIHEDRAL : 13.894 573 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 7KC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30598 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.12050 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 1.77500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.640 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: 3F74 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 3350 AND 0.1 M POTASSIUM REMARK 280 PHOSPHATE DIBASIC, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.42933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.21467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.21467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.42933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 541 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 590 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 648 LIES ON A SPECIAL POSITION. 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 ILE C 309 REMARK 465 GLU C 310 REMARK 465 GLY C 311 REMARK 465 THR C 312 REMARK 465 SER C 313 REMARK 465 LYS C 314 REMARK 465 GLN C 315 REMARK 465 ASP C 316 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 C 542 O HOH C 635 2.05 REMARK 500 O HOH C 515 O HOH C 585 2.12 REMARK 500 O HOH C 620 O HOH C 635 2.17 REMARK 500 O HOH C 595 O HOH C 633 2.18 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 SER C 174 -100.76 -148.71 REMARK 500 SER C 176 -167.58 -121.65 REMARK 500 LEU C 204 -135.15 -127.69 REMARK 500 LEU C 205 -157.68 -89.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 139 OG REMARK 620 2 SER C 141 OG 88.0 REMARK 620 3 ASP C 239 OD1 92.1 86.8 REMARK 620 4 HOH C 503 O 89.9 91.7 177.5 REMARK 620 5 HOH C 538 O 176.6 88.7 88.8 89.1 REMARK 620 6 HOH C 544 O 87.5 169.8 84.2 97.5 95.9 REMARK 620 N 1 2 3 4 5 DBREF 7KC3 C 124 316 UNP P20701 ITAL_HUMAN 149 341 SEQADV 7KC3 GLY C 121 UNP P20701 EXPRESSION TAG SEQADV 7KC3 HIS C 122 UNP P20701 EXPRESSION TAG SEQADV 7KC3 MET C 123 UNP P20701 EXPRESSION TAG SEQRES 1 C 196 GLY HIS MET GLU CYS ILE LYS GLY ASN VAL ASP LEU VAL SEQRES 2 C 196 PHE LEU PHE ASP GLY SER MET SER LEU GLN PRO ASP GLU SEQRES 3 C 196 PHE GLN LYS ILE LEU ASP PHE MET LYS ASP VAL MET LYS SEQRES 4 C 196 LYS LEU SER ASN THR SER TYR GLN PHE ALA ALA VAL GLN SEQRES 5 C 196 PHE SER THR SER TYR LYS THR GLU PHE ASP PHE SER ASP SEQRES 6 C 196 TYR VAL LYS ARG LYS ASP PRO ASP ALA LEU LEU LYS HIS SEQRES 7 C 196 VAL LYS HIS MET LEU LEU LEU THR ASN THR PHE GLY ALA SEQRES 8 C 196 ILE ASN TYR VAL ALA THR GLU VAL PHE ARG GLU GLU LEU SEQRES 9 C 196 GLY ALA ARG PRO ASP ALA THR LYS VAL LEU ILE ILE ILE SEQRES 10 C 196 THR ASP GLY GLU ALA THR ASP SER GLY ASN ILE ASP ALA SEQRES 11 C 196 ALA LYS ASP ILE ILE ARG TYR ILE ILE GLY ILE GLY LYS SEQRES 12 C 196 HIS PHE GLN THR LYS GLU SER GLN GLU THR LEU HIS LYS SEQRES 13 C 196 PHE ALA SER LYS PRO ALA SER GLU PHE VAL LYS ILE LEU SEQRES 14 C 196 ASP THR PHE GLU LYS LEU LYS ASP LEU PHE THR GLU LEU SEQRES 15 C 196 GLN LYS LYS ILE TYR VAL ILE GLU GLY THR SER LYS GLN SEQRES 16 C 196 ASP HET MG C 401 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *159(H2 O) HELIX 1 AA1 GLY C 121 ILE C 126 1 6 HELIX 2 AA2 GLN C 143 LEU C 161 1 19 HELIX 3 AA3 ASP C 182 ARG C 189 1 8 HELIX 4 AA4 ASP C 191 LEU C 196 1 6 HELIX 5 AA5 ASN C 207 VAL C 219 1 13 HELIX 6 AA6 ARG C 221 GLY C 225 5 5 HELIX 7 AA7 ILE C 248 LYS C 252 5 5 HELIX 8 AA8 LYS C 263 GLN C 266 5 4 HELIX 9 AA9 THR C 267 THR C 273 1 7 HELIX 10 AB1 LEU C 274 ALA C 278 5 5 HELIX 11 AB2 PRO C 281 PHE C 285 1 5 HELIX 12 AB3 GLU C 293 LYS C 304 1 12 SHEET 1 AA1 6 TYR C 177 PHE C 181 0 SHEET 2 AA1 6 TYR C 166 PHE C 173 -1 N GLN C 172 O LYS C 178 SHEET 3 AA1 6 VAL C 130 ASP C 137 1 N LEU C 132 O GLN C 167 SHEET 4 AA1 6 THR C 231 THR C 238 1 O ILE C 235 N LEU C 135 SHEET 5 AA1 6 ILE C 254 ILE C 261 1 O ILE C 259 N ILE C 236 SHEET 6 AA1 6 VAL C 286 LEU C 289 1 O LYS C 287 N ILE C 258 LINK OG SER C 139 MG MG C 401 1555 1555 2.14 LINK OG SER C 141 MG MG C 401 1555 1555 2.14 LINK OD1 ASP C 239 MG MG C 401 1555 1555 2.05 LINK MG MG C 401 O HOH C 503 1555 2654 2.10 LINK MG MG C 401 O HOH C 538 1555 1555 2.07 LINK MG MG C 401 O HOH C 544 1555 1555 2.09 CISPEP 1 LYS C 280 PRO C 281 0 -2.65 CRYST1 104.896 104.896 51.644 90.00 90.00 120.00 P 32 2 1 6 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 0.009533 0.005504 0.000000 0.00000 SCALE2 0.000000 0.011008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019363 0.00000