HEADER IMMUNE SYSTEM 22-OCT-14 4RMW TITLE CRYSTAL STRUCTURE OF THE D76A BETA-2 MICROGLOBULIN MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-119; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: B2M, CDABP0092, HDCMA22P, NM_004048; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNOGLOBIN, BETA-SANDWITCH, AMYLOIDOSIS, PATHOLOGIC MUTATION, KEYWDS 2 GENETIC DISEASE, MHC CLASS I, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.DE ROSA,M.BOLOGNESI,S.RICAGNO REVDAT 3 20-SEP-23 4RMW 1 REMARK SEQADV REVDAT 2 27-JUN-18 4RMW 1 JRNL REVDAT 1 18-NOV-15 4RMW 0 JRNL AUTH T.LE MARCHAND,M.DE ROSA,N.SALVI,B.M.SALA,L.B.ANDREAS, JRNL AUTH 2 E.BARBET-MASSIN,P.SORMANNI,A.BARBIROLI,R.PORCARI, JRNL AUTH 3 C.SOUSA MOTA,D.DE SANCTIS,M.BOLOGNESI,L.EMSLEY,V.BELLOTTI, JRNL AUTH 4 M.BLACKLEDGE,C.CAMILLONI,G.PINTACUDA,S.RICAGNO JRNL TITL CONFORMATIONAL DYNAMICS IN CRYSTALS REVEAL THE MOLECULAR JRNL TITL 2 BASES FOR D76N BETA-2 MICROGLOBULIN AGGREGATION PROPENSITY. JRNL REF NAT COMMUN V. 9 1658 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29695721 JRNL DOI 10.1038/S41467-018-04078-Y REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 38.6079 - 3.3737 0.99 1344 149 0.1615 0.1954 REMARK 3 2 3.3737 - 2.6780 0.99 1294 145 0.1745 0.2092 REMARK 3 3 2.6780 - 2.3395 1.00 1288 142 0.1783 0.1956 REMARK 3 4 2.3395 - 2.1257 1.00 1290 144 0.1667 0.1974 REMARK 3 5 2.1257 - 1.9733 1.00 1250 138 0.1685 0.2223 REMARK 3 6 1.9733 - 1.8570 1.00 1306 146 0.1705 0.1863 REMARK 3 7 1.8570 - 1.7640 1.00 1266 141 0.1783 0.2070 REMARK 3 8 1.7640 - 1.6872 1.00 1268 140 0.1817 0.2250 REMARK 3 9 1.6872 - 1.6222 1.00 1265 141 0.2019 0.2478 REMARK 3 10 1.6222 - 1.5663 1.00 1286 143 0.1990 0.2458 REMARK 3 11 1.5663 - 1.5173 1.00 1258 140 0.2100 0.2329 REMARK 3 12 1.5173 - 1.4739 1.00 1265 140 0.2194 0.2441 REMARK 3 13 1.4739 - 1.4351 1.00 1266 141 0.2488 0.2869 REMARK 3 14 1.4351 - 1.4000 1.00 1282 142 0.2622 0.3138 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.680 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 : 0.020 1003 REMARK 3 ANGLE : 1.948 1374 REMARK 3 CHIRALITY : 0.112 142 REMARK 3 PLANARITY : 0.011 182 REMARK 3 DIHEDRAL : 15.028 390 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6379 -20.5590 -19.5847 REMARK 3 T TENSOR REMARK 3 T11: 0.0772 T22: 0.0571 REMARK 3 T33: 0.0992 T12: -0.0041 REMARK 3 T13: 0.0175 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 7.6752 L22: 1.6527 REMARK 3 L33: 5.2840 L12: 3.2842 REMARK 3 L13: 6.2642 L23: 2.8680 REMARK 3 S TENSOR REMARK 3 S11: 0.0352 S12: 0.1139 S13: -0.0929 REMARK 3 S21: -0.0357 S22: 0.0599 S23: -0.0325 REMARK 3 S31: 0.0227 S32: 0.0787 S33: -0.1823 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 13 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9963 -4.9824 -12.7827 REMARK 3 T TENSOR REMARK 3 T11: 0.3458 T22: 0.2561 REMARK 3 T33: 0.3118 T12: -0.1092 REMARK 3 T13: 0.1178 T23: -0.1244 REMARK 3 L TENSOR REMARK 3 L11: 5.8509 L22: 7.4525 REMARK 3 L33: 0.1235 L12: -2.1503 REMARK 3 L13: 0.5932 L23: 0.4282 REMARK 3 S TENSOR REMARK 3 S11: 0.3631 S12: -0.8879 S13: 1.1574 REMARK 3 S21: 0.4540 S22: -0.0145 S23: -0.3998 REMARK 3 S31: -1.2318 S32: 0.5807 S33: -0.1880 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0275 -13.6877 -15.2306 REMARK 3 T TENSOR REMARK 3 T11: 0.0786 T22: 0.0392 REMARK 3 T33: 0.0805 T12: -0.0157 REMARK 3 T13: 0.0277 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 3.7910 L22: 1.7276 REMARK 3 L33: 3.8479 L12: 1.1594 REMARK 3 L13: 2.8039 L23: 1.5033 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: -0.0576 S13: 0.0943 REMARK 3 S21: 0.0496 S22: 0.0139 S23: -0.0135 REMARK 3 S31: -0.1080 S32: 0.0872 S33: -0.0148 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5150 -7.2915 -11.8626 REMARK 3 T TENSOR REMARK 3 T11: 0.3496 T22: 0.2154 REMARK 3 T33: 0.2719 T12: 0.0250 REMARK 3 T13: 0.0011 T23: -0.0635 REMARK 3 L TENSOR REMARK 3 L11: 1.5298 L22: 0.7407 REMARK 3 L33: 4.9266 L12: -0.0073 REMARK 3 L13: 1.1030 L23: -1.8550 REMARK 3 S TENSOR REMARK 3 S11: -0.2158 S12: -0.3777 S13: 0.4779 REMARK 3 S21: 0.3746 S22: -0.2220 S23: -0.0630 REMARK 3 S31: -1.2924 S32: -0.4784 S33: 0.2794 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7261 -17.2336 -32.7321 REMARK 3 T TENSOR REMARK 3 T11: 0.2431 T22: 0.2893 REMARK 3 T33: 0.0859 T12: 0.0211 REMARK 3 T13: 0.0048 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 5.5047 L22: 5.2726 REMARK 3 L33: 7.3503 L12: 4.0948 REMARK 3 L13: 6.3476 L23: 4.9922 REMARK 3 S TENSOR REMARK 3 S11: 0.3342 S12: 0.5780 S13: -0.2313 REMARK 3 S21: -0.4166 S22: -0.1845 S23: -0.0160 REMARK 3 S31: 0.8349 S32: -0.5387 S33: -0.1107 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9361 -9.8370 -16.0189 REMARK 3 T TENSOR REMARK 3 T11: 0.1595 T22: 0.1079 REMARK 3 T33: 0.1587 T12: -0.0298 REMARK 3 T13: 0.0196 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 4.4001 L22: 5.9938 REMARK 3 L33: 7.5518 L12: 2.1189 REMARK 3 L13: 3.8663 L23: 4.4198 REMARK 3 S TENSOR REMARK 3 S11: 0.0862 S12: -0.0508 S13: 0.0991 REMARK 3 S21: 0.4730 S22: 0.0838 S23: -0.3051 REMARK 3 S31: -0.1265 S32: 0.3524 S33: -0.1935 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2690 -13.9968 1.7336 REMARK 3 T TENSOR REMARK 3 T11: 0.5860 T22: 0.5292 REMARK 3 T33: 0.3621 T12: -0.1433 REMARK 3 T13: -0.2103 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 2.0730 L22: 0.5577 REMARK 3 L33: 2.6282 L12: -1.0659 REMARK 3 L13: -2.3288 L23: 1.1985 REMARK 3 S TENSOR REMARK 3 S11: 0.1446 S12: -0.5371 S13: -0.0414 REMARK 3 S21: 0.7929 S22: 0.2748 S23: -0.9101 REMARK 3 S31: 0.2377 S32: 1.3868 S33: -0.3414 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3307 -18.6441 -11.6458 REMARK 3 T TENSOR REMARK 3 T11: 0.1003 T22: 0.1267 REMARK 3 T33: 0.0802 T12: -0.0531 REMARK 3 T13: 0.0151 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 6.3071 L22: 0.7314 REMARK 3 L33: 1.1159 L12: 1.7211 REMARK 3 L13: 1.8936 L23: 0.1049 REMARK 3 S TENSOR REMARK 3 S11: 0.3309 S12: -0.7683 S13: -0.0505 REMARK 3 S21: 0.2771 S22: -0.3483 S23: 0.0157 REMARK 3 S31: 0.3347 S32: -0.3737 S33: 0.0482 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2370 -20.0694 -6.2060 REMARK 3 T TENSOR REMARK 3 T11: 0.1344 T22: 0.1149 REMARK 3 T33: 0.1742 T12: -0.0041 REMARK 3 T13: -0.0253 T23: 0.0508 REMARK 3 L TENSOR REMARK 3 L11: 7.6141 L22: 3.3306 REMARK 3 L33: 3.7925 L12: 1.0782 REMARK 3 L13: 0.0685 L23: -1.5306 REMARK 3 S TENSOR REMARK 3 S11: 0.2723 S12: -0.5299 S13: -0.9053 REMARK 3 S21: -0.0302 S22: -0.2018 S23: -0.2940 REMARK 3 S31: 0.2250 S32: 0.2736 S33: -0.0561 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 4RMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000087543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 44.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 2YXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG4000, 15% GLYCEROL, 0.2 M REMARK 280 AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.81200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.49600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.81200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.49600 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 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 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 LYS A 58 CG CD CE NZ 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 270 O HOH A 314 2.05 REMARK 500 ND2 ASN A 83 O HOH A 257 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O SER A 11 OG SER A 57 2554 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 25 CB CYS A 25 SG -0.131 REMARK 500 CYS A 80 CB CYS A 80 SG 0.171 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 80 CA - CB - SG ANGL. DEV. = 7.9 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 57 -79.07 -121.69 REMARK 500 SER A 61 116.68 -165.27 REMARK 500 THR A 73 155.86 67.11 REMARK 500 LYS A 75 -71.17 -81.27 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 PGE A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YXF RELATED DB: PDB REMARK 900 RELATED ID: 4FXL RELATED DB: PDB REMARK 900 RELATED ID: 4RMQ RELATED DB: PDB REMARK 900 RELATED ID: 4RMR RELATED DB: PDB REMARK 900 RELATED ID: 4RMS RELATED DB: PDB REMARK 900 RELATED ID: 4RMT RELATED DB: PDB REMARK 900 RELATED ID: 4RMU RELATED DB: PDB REMARK 900 RELATED ID: 4RMV RELATED DB: PDB DBREF 4RMW A 1 99 UNP P61769 B2MG_HUMAN 21 119 SEQADV 4RMW MET A 0 UNP P61769 INITIATING METHIONINE SEQADV 4RMW ALA A 76 UNP P61769 ASP 96 ENGINEERED MUTATION SEQRES 1 A 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 A 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 A 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 A 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 A 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 A 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ALA GLU SEQRES 7 A 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 A 100 LYS ILE VAL LYS TRP ASP ARG ASP MET HET PGE A 101 10 HET ACT A 102 4 HETNAM PGE TRIETHYLENE GLYCOL HETNAM ACT ACETATE ION FORMUL 2 PGE C6 H14 O4 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *115(H2 O) HELIX 1 1 PRO A 14 GLY A 18 5 5 SHEET 1 A 4 LYS A 6 ARG A 12 0 SHEET 2 A 4 ASN A 21 PHE A 30 -1 O ASN A 24 N TYR A 10 SHEET 3 A 4 PHE A 62 PHE A 70 -1 O LEU A 64 N VAL A 27 SHEET 4 A 4 HIS A 51 PHE A 56 -1 N ASP A 53 O LEU A 65 SHEET 1 B 4 GLU A 44 ARG A 45 0 SHEET 2 B 4 GLU A 36 LYS A 41 -1 N LYS A 41 O GLU A 44 SHEET 3 B 4 TYR A 78 ASN A 83 -1 O ARG A 81 N ASP A 38 SHEET 4 B 4 LYS A 91 LYS A 94 -1 O VAL A 93 N CYS A 80 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.03 CISPEP 1 HIS A 31 PRO A 32 0 -6.86 SITE 1 AC1 3 TYR A 10 TYR A 26 SER A 28 SITE 1 AC2 9 LYS A 41 THR A 71 PRO A 72 THR A 73 SITE 2 AC2 9 TYR A 78 ASP A 96 ARG A 97 ASP A 98 SITE 3 AC2 9 HOH A 252 CRYST1 77.624 28.992 56.293 90.00 127.20 90.00 C 1 2 1 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 0.012883 0.000000 0.009777 0.00000 SCALE2 0.000000 0.034492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022301 0.00000