PDB Short entry for 1MJN HEADER IMMUNE SYSTEM 28-AUG-02 1MJN TITLE CRYSTAL STRUCTURE OF THE INTERMEDIATE AFFINITY AL I DOMAIN MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-L; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: INTERMEDIATE AFFINITY AL I DOMAIN; COMPND 5 SYNONYM: LEUKOCYTE ADHESION GLYCOPROTEIN LFA-1 ALPHA CHAIN, LEUKOCYTE COMPND 6 FUNCTION ASSOCIATED MOLECULE 1, ALPHA CHAIN, CD11A; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ROSSMANN FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.SHIMAOKA,T.XIAO,J.H.LIU,Y.T.YANG,Y.C.DONG,C.D.JUN,A.MCCORMACK, AUTHOR 2 R.G.ZHANG,J.H.WANG,T.A.SPRINGER REVDAT 4 27-OCT-21 1MJN 1 REMARK SEQADV LINK REVDAT 3 19-MAY-10 1MJN 1 SOURCE REVDAT 2 24-FEB-09 1MJN 1 VERSN REVDAT 1 28-JAN-03 1MJN 0 JRNL AUTH M.SHIMAOKA,T.XIAO,J.H.LIU,Y.T.YANG,Y.C.DONG,C.D.JUN, JRNL AUTH 2 A.MCCORMACK,R.G.ZHANG,A.JOACHIMIAK,J.TAKAGI,J.H.WANG, JRNL AUTH 3 T.A.SPRINGER JRNL TITL STRUCTURES OF THE ALPHAL I DOMAIN AND ITS COMPLEX WITH JRNL TITL 2 ICAM-1 REVEAL A SHAPE-SHIFTING PATHWAY FOR INTEGRIN JRNL TITL 3 REGULATION JRNL REF CELL(CAMBRIDGE,MASS.) V. 112 99 2003 JRNL REFN ISSN 0092-8674 JRNL PMID 12526797 JRNL DOI 10.1016/S0092-8674(02)01257-6 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.156 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3516 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 31703 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.140 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2764 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 24644 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1432 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 322 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : 0.35200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LFA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MGCL2, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.18700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.45450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.69950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.45450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.18700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.69950 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 177 CB - CG - CD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 TYR A 177 CB - CG - CD1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 189 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 TYR A 214 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 256 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 TYR A 257 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 297 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES 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 A 174 -97.59 -150.73 REMARK 500 LEU A 204 -133.77 -127.48 REMARK 500 ASP A 244 -164.28 -102.29 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 139 OG REMARK 620 2 SER A 141 OG 88.0 REMARK 620 3 ASP A 239 OD1 89.9 85.4 REMARK 620 4 HOH A2265 O 175.2 87.3 90.7 REMARK 620 5 HOH A2266 O 90.5 92.2 177.6 88.8 REMARK 620 6 HOH A2267 O 87.2 168.5 84.1 97.5 98.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 DBREF 1MJN A 128 306 UNP P20701 ITAL_HUMAN 153 331 SEQADV 1MJN CYS A 161 UNP P20701 LEU 186 ENGINEERED MUTATION SEQADV 1MJN CYS A 299 UNP P20701 PHE 324 ENGINEERED MUTATION SEQRES 1 A 179 GLY ASN VAL ASP LEU VAL PHE LEU PHE ASP GLY SER MET SEQRES 2 A 179 SER LEU GLN PRO ASP GLU PHE GLN LYS ILE LEU ASP PHE SEQRES 3 A 179 MET LYS ASP VAL MET LYS LYS CYS SER ASN THR SER TYR SEQRES 4 A 179 GLN PHE ALA ALA VAL GLN PHE SER THR SER TYR LYS THR SEQRES 5 A 179 GLU PHE ASP PHE SER ASP TYR VAL LYS ARG LYS ASP PRO SEQRES 6 A 179 ASP ALA LEU LEU LYS HIS VAL LYS HIS MET LEU LEU LEU SEQRES 7 A 179 THR ASN THR PHE GLY ALA ILE ASN TYR VAL ALA THR GLU SEQRES 8 A 179 VAL PHE ARG GLU GLU LEU GLY ALA ARG PRO ASP ALA THR SEQRES 9 A 179 LYS VAL LEU ILE ILE ILE THR ASP GLY GLU ALA THR ASP SEQRES 10 A 179 SER GLY ASN ILE ASP ALA ALA LYS ASP ILE ILE ARG TYR SEQRES 11 A 179 ILE ILE GLY ILE GLY LYS HIS PHE GLN THR LYS GLU SER SEQRES 12 A 179 GLN GLU THR LEU HIS LYS PHE ALA SER LYS PRO ALA SER SEQRES 13 A 179 GLU PHE VAL LYS ILE LEU ASP THR PHE GLU LYS LEU LYS SEQRES 14 A 179 ASP LEU CYS THR GLU LEU GLN LYS LYS ILE HET MG A1001 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *322(H2 O) HELIX 1 1 GLN A 143 CYS A 161 1 19 HELIX 2 2 ASP A 182 LYS A 190 1 9 HELIX 3 3 ASP A 191 LYS A 197 1 7 HELIX 4 4 ASN A 207 VAL A 219 1 13 HELIX 5 5 ARG A 221 GLY A 225 5 5 HELIX 6 6 ILE A 248 LYS A 252 5 5 HELIX 7 7 LYS A 263 GLN A 266 5 4 HELIX 8 8 THR A 267 THR A 273 1 7 HELIX 9 9 LEU A 274 ALA A 278 5 5 HELIX 10 10 PRO A 281 PHE A 285 1 5 HELIX 11 11 THR A 291 LEU A 295 5 5 HELIX 12 12 ASP A 297 ILE A 306 1 10 SHEET 1 A 6 TYR A 177 PHE A 181 0 SHEET 2 A 6 TYR A 166 PHE A 173 -1 N ALA A 170 O PHE A 181 SHEET 3 A 6 VAL A 130 ASP A 137 1 N PHE A 134 O VAL A 171 SHEET 4 A 6 THR A 231 THR A 238 1 O ILE A 237 N LEU A 135 SHEET 5 A 6 ILE A 255 ILE A 261 1 O ILE A 259 N ILE A 236 SHEET 6 A 6 VAL A 286 LEU A 289 1 O LYS A 287 N ILE A 258 SSBOND 1 CYS A 161 CYS A 299 1555 1555 2.08 LINK OG SER A 139 MG MG A1001 1555 1555 2.21 LINK OG SER A 141 MG MG A1001 1555 1555 2.07 LINK OD1 ASP A 239 MG MG A1001 1555 1555 2.07 LINK MG MG A1001 O HOH A2265 1555 1555 2.08 LINK MG MG A1001 O HOH A2266 1555 1555 2.07 LINK MG MG A1001 O HOH A2267 1555 1555 2.04 CISPEP 1 LYS A 280 PRO A 281 0 -0.06 SITE 1 AC1 6 SER A 139 SER A 141 ASP A 239 HOH A2265 SITE 2 AC1 6 HOH A2266 HOH A2267 CRYST1 40.374 57.399 66.909 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 0.024768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017422 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014946 0.00000