HEADER HYDROLASE 05-OCT-13 4N2N TITLE CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (E354A, 10 MM CA2+) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-ARGININE DEIMINASE TYPE-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAD-H19, PEPTIDYLARGININE DEIMINASE II, PROTEIN-ARGININE COMPND 5 DEIMINASE TYPE II; COMPND 6 EC: 3.5.3.15; COMPND 7 ENGINEERED: YES; COMPND 8 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: PADI2, KIAA0994, PDI2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEIMINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.J.SLADE,X.ZHANG,P.FANG,C.J.DREYTON,Y.ZHANG,M.L.GROSS,M.GUO, AUTHOR 2 S.A.COONROD,P.R.THOMPSON REVDAT 3 20-SEP-23 4N2N 1 REMARK SEQADV LINK REVDAT 2 06-MAY-15 4N2N 1 JRNL REVDAT 1 04-FEB-15 4N2N 0 JRNL AUTH D.J.SLADE,P.FANG,C.J.DREYTON,Y.ZHANG,J.FUHRMANN,D.REMPEL, JRNL AUTH 2 B.D.BAX,S.A.COONROD,H.D.LEWIS,M.GUO,M.L.GROSS,P.R.THOMPSON JRNL TITL PROTEIN ARGININE DEIMINASE 2 BINDS CALCIUM IN AN ORDERED JRNL TITL 2 FASHION: IMPLICATIONS FOR INHIBITOR DESIGN. JRNL REF ACS CHEM.BIOL. V. 10 1043 2015 JRNL REFN ISSN 1554-8929 JRNL PMID 25621824 JRNL DOI 10.1021/CB500933J REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 70612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3569 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 38.0715 - 3.8768 1.00 6930 384 0.1510 0.1687 REMARK 3 2 3.8768 - 3.0775 1.00 6779 360 0.1564 0.1756 REMARK 3 3 3.0775 - 2.6886 1.00 6751 354 0.1707 0.2029 REMARK 3 4 2.6886 - 2.4428 1.00 6710 355 0.1771 0.2183 REMARK 3 5 2.4428 - 2.2678 0.99 6705 365 0.1633 0.2215 REMARK 3 6 2.2678 - 2.1341 0.99 6654 337 0.1713 0.2050 REMARK 3 7 2.1341 - 2.0272 0.99 6641 381 0.1734 0.2306 REMARK 3 8 2.0272 - 1.9390 0.99 6644 334 0.1887 0.2522 REMARK 3 9 1.9390 - 1.8643 0.99 6618 345 0.2241 0.2651 REMARK 3 10 1.8643 - 1.8000 0.99 6611 354 0.2761 0.3076 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 : 0.35 REMARK 3 B_SOL : 45.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.04520 REMARK 3 B22 (A**2) : 8.29490 REMARK 3 B33 (A**2) : -1.24970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.88230 REMARK 3 B23 (A**2) : 0.00000 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 5448 REMARK 3 ANGLE : 1.237 7458 REMARK 3 CHIRALITY : 0.105 820 REMARK 3 PLANARITY : 0.007 954 REMARK 3 DIHEDRAL : 13.784 1988 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 4N2N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70612 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 38.063 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : NULL 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) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 4N25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% MPD, 50 MM MES, PH 5.6, 0.12 M REMARK 280 SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP 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 101.60000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 101.60000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.81500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 52910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -168.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A1290 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 HIS A -5 REMARK 465 ILE A -4 REMARK 465 GLU A -3 REMARK 465 GLY A -2 REMARK 465 ARG A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 340 REMARK 465 TYR A 341 REMARK 465 LEU A 342 REMARK 465 ASN A 343 REMARK 465 ARG A 344 REMARK 465 GLY A 345 REMARK 465 LEU A 398 REMARK 465 PHE A 399 REMARK 465 SER A 669 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 LEU A 2 CG CD1 CD2 REMARK 470 ARG A 3 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CE NZ REMARK 470 TRP A 49 CE3 CZ2 CZ3 CH2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 GLU A 101 CG CD OE1 OE2 REMARK 470 LEU A 162 CG CD1 CD2 REMARK 470 ARG A 225 CZ NH1 NH2 REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 LYS A 315 CG CD CE NZ REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 376 CG OD1 ND2 REMARK 470 LEU A 377 CG CD1 CD2 REMARK 470 ASP A 379 CG OD1 OD2 REMARK 470 PHE A 380 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 396 CG CD OE1 OE2 REMARK 470 GLU A 400 CG CD OE1 OE2 REMARK 470 LYS A 485 CG CD CE NZ REMARK 470 LYS A 499 CG CD CE NZ REMARK 470 ARG A 525 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 644 CG CD OE1 OE2 REMARK 470 ARG A 668 CG CD NE CZ NH1 NH2 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 NE ARG A 225 O HOH A 1394 2.15 REMARK 500 NZ LYS A 175 O HOH A 1418 2.16 REMARK 500 O ILE A 513 O HOH A 1042 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 PRO A 220 -179.44 -68.71 REMARK 500 ARG A 233 19.59 56.75 REMARK 500 MET A 276 -61.79 -98.40 REMARK 500 LEU A 377 -61.95 -108.66 REMARK 500 GLN A 455 -27.22 72.30 REMARK 500 ALA A 458 68.08 33.90 REMARK 500 ASP A 595 -122.40 44.54 REMARK 500 ASP A 595 -122.55 43.22 REMARK 500 HIS A 639 -4.93 66.18 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 CA A 706 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 123 OD1 REMARK 620 2 ASP A 125 OD1 86.1 REMARK 620 3 ASP A 127 OD1 82.3 90.1 REMARK 620 4 VAL A 129 O 84.9 169.3 94.4 REMARK 620 5 GLU A 131 OE1 102.4 91.0 175.3 85.3 REMARK 620 6 HOH A1230 O 167.8 87.8 87.2 102.1 88.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 705 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 154 OD1 REMARK 620 2 ASP A 156 OD1 81.5 REMARK 620 3 GLU A 158 OE2 163.6 97.7 REMARK 620 4 ASP A 166 OD1 105.0 81.7 91.0 REMARK 620 5 ASP A 177 OD1 89.1 161.3 95.8 85.3 REMARK 620 6 ASP A 180 OD2 89.7 92.6 73.9 163.1 103.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 704 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 156 OD2 REMARK 620 2 GLU A 158 OE2 80.8 REMARK 620 3 ASP A 180 OD2 89.5 68.2 REMARK 620 4 ASP A 180 OD1 109.3 118.6 52.2 REMARK 620 5 ASP A 389 OD1 87.0 156.6 132.0 84.2 REMARK 620 6 HOH A 858 O 172.6 92.0 89.4 75.6 99.1 REMARK 620 7 HOH A 878 O 93.1 77.6 144.8 153.6 83.2 83.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 709 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 166 O REMARK 620 2 ASP A 169 OD1 82.8 REMARK 620 3 LYS A 171 O 165.8 83.9 REMARK 620 4 HOH A 823 O 81.3 70.8 89.7 REMARK 620 5 HOH A 965 O 107.5 142.4 86.1 145.4 REMARK 620 6 HOH A1110 O 86.4 72.6 94.3 142.4 72.1 REMARK 620 7 HOH A1359 O 87.1 145.6 101.3 75.2 72.0 139.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 709 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N20 RELATED DB: PDB REMARK 900 RELATED ID: 4N22 RELATED DB: PDB REMARK 900 RELATED ID: 4N24 RELATED DB: PDB REMARK 900 RELATED ID: 4N25 RELATED DB: PDB REMARK 900 RELATED ID: 4N26 RELATED DB: PDB REMARK 900 RELATED ID: 4N28 RELATED DB: PDB REMARK 900 RELATED ID: 4N2A RELATED DB: PDB REMARK 900 RELATED ID: 4N2B RELATED DB: PDB REMARK 900 RELATED ID: 4N2C RELATED DB: PDB REMARK 900 RELATED ID: 4N2D RELATED DB: PDB REMARK 900 RELATED ID: 4N2E RELATED DB: PDB REMARK 900 RELATED ID: 4N2F RELATED DB: PDB REMARK 900 RELATED ID: 4N2G RELATED DB: PDB REMARK 900 RELATED ID: 4N2H RELATED DB: PDB REMARK 900 RELATED ID: 4N2I RELATED DB: PDB REMARK 900 RELATED ID: 4N2K RELATED DB: PDB REMARK 900 RELATED ID: 4N2L RELATED DB: PDB REMARK 900 RELATED ID: 4N2M RELATED DB: PDB DBREF 4N2N A 1 665 UNP Q9Y2J8 PADI2_HUMAN 1 665 SEQADV 4N2N MET A -20 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N GLY A -19 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -18 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -17 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -16 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -15 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -14 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -13 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -12 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -11 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -10 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -9 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N SER A -8 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N SER A -7 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N GLY A -6 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A -5 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N ILE A -4 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N GLU A -3 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N GLY A -2 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N ARG A -1 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N HIS A 0 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N ALA A 354 UNP Q9Y2J8 GLU 354 ENGINEERED MUTATION SEQADV 4N2N SER A 666 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N ARG A 667 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N ARG A 668 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2N SER A 669 UNP Q9Y2J8 EXPRESSION TAG SEQRES 1 A 690 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 690 SER GLY HIS ILE GLU GLY ARG HIS MET LEU ARG GLU ARG SEQRES 3 A 690 THR VAL ARG LEU GLN TYR GLY SER ARG VAL GLU ALA VAL SEQRES 4 A 690 TYR VAL LEU GLY THR TYR LEU TRP THR ASP VAL TYR SER SEQRES 5 A 690 ALA ALA PRO ALA GLY ALA GLN THR PHE SER LEU LYS HIS SEQRES 6 A 690 SER GLU HIS VAL TRP VAL GLU VAL VAL ARG ASP GLY GLU SEQRES 7 A 690 ALA GLU GLU VAL ALA THR ASN GLY LYS GLN ARG TRP LEU SEQRES 8 A 690 LEU SER PRO SER THR THR LEU ARG VAL THR MET SER GLN SEQRES 9 A 690 ALA SER THR GLU ALA SER SER ASP LYS VAL THR VAL ASN SEQRES 10 A 690 TYR TYR ASP GLU GLU GLY SER ILE PRO ILE ASP GLN ALA SEQRES 11 A 690 GLY LEU PHE LEU THR ALA ILE GLU ILE SER LEU ASP VAL SEQRES 12 A 690 ASP ALA ASP ARG ASP GLY VAL VAL GLU LYS ASN ASN PRO SEQRES 13 A 690 LYS LYS ALA SER TRP THR TRP GLY PRO GLU GLY GLN GLY SEQRES 14 A 690 ALA ILE LEU LEU VAL ASN CYS ASP ARG GLU THR PRO TRP SEQRES 15 A 690 LEU PRO LYS GLU ASP CYS ARG ASP GLU LYS VAL TYR SER SEQRES 16 A 690 LYS GLU ASP LEU LYS ASP MET SER GLN MET ILE LEU ARG SEQRES 17 A 690 THR LYS GLY PRO ASP ARG LEU PRO ALA GLY TYR GLU ILE SEQRES 18 A 690 VAL LEU TYR ILE SER MET SER ASP SER ASP LYS VAL GLY SEQRES 19 A 690 VAL PHE TYR VAL GLU ASN PRO PHE PHE GLY GLN ARG TYR SEQRES 20 A 690 ILE HIS ILE LEU GLY ARG ARG LYS LEU TYR HIS VAL VAL SEQRES 21 A 690 LYS TYR THR GLY GLY SER ALA GLU LEU LEU PHE PHE VAL SEQRES 22 A 690 GLU GLY LEU CYS PHE PRO ASP GLU GLY PHE SER GLY LEU SEQRES 23 A 690 VAL SER ILE HIS VAL SER LEU LEU GLU TYR MET ALA GLN SEQRES 24 A 690 ASP ILE PRO LEU THR PRO ILE PHE THR ASP THR VAL ILE SEQRES 25 A 690 PHE ARG ILE ALA PRO TRP ILE MET THR PRO ASN ILE LEU SEQRES 26 A 690 PRO PRO VAL SER VAL PHE VAL CYS CYS MET LYS ASP ASN SEQRES 27 A 690 TYR LEU PHE LEU LYS GLU VAL LYS ASN LEU VAL GLU LYS SEQRES 28 A 690 THR ASN CYS GLU LEU LYS VAL CYS PHE GLN TYR LEU ASN SEQRES 29 A 690 ARG GLY ASP ARG TRP ILE GLN ASP GLU ILE ALA PHE GLY SEQRES 30 A 690 TYR ILE GLU ALA PRO HIS LYS GLY PHE PRO VAL VAL LEU SEQRES 31 A 690 ASP SER PRO ARG ASP GLY ASN LEU LYS ASP PHE PRO VAL SEQRES 32 A 690 LYS GLU LEU LEU GLY PRO ASP PHE GLY TYR VAL THR ARG SEQRES 33 A 690 GLU PRO LEU PHE GLU SER VAL THR SER LEU ASP SER PHE SEQRES 34 A 690 GLY ASN LEU GLU VAL SER PRO PRO VAL THR VAL ASN GLY SEQRES 35 A 690 LYS THR TYR PRO LEU GLY ARG ILE LEU ILE GLY SER SER SEQRES 36 A 690 PHE PRO LEU SER GLY GLY ARG ARG MET THR LYS VAL VAL SEQRES 37 A 690 ARG ASP PHE LEU LYS ALA GLN GLN VAL GLN ALA PRO VAL SEQRES 38 A 690 GLU LEU TYR SER ASP TRP LEU THR VAL GLY HIS VAL ASP SEQRES 39 A 690 GLU PHE MET SER PHE VAL PRO ILE PRO GLY THR LYS LYS SEQRES 40 A 690 PHE LEU LEU LEU MET ALA SER THR SER ALA CYS TYR LYS SEQRES 41 A 690 LEU PHE ARG GLU LYS GLN LYS ASP GLY HIS GLY GLU ALA SEQRES 42 A 690 ILE MET PHE LYS GLY LEU GLY GLY MET SER SER LYS ARG SEQRES 43 A 690 ILE THR ILE ASN LYS ILE LEU SER ASN GLU SER LEU VAL SEQRES 44 A 690 GLN GLU ASN LEU TYR PHE GLN ARG CYS LEU ASP TRP ASN SEQRES 45 A 690 ARG ASP ILE LEU LYS LYS GLU LEU GLY LEU THR GLU GLN SEQRES 46 A 690 ASP ILE ILE ASP LEU PRO ALA LEU PHE LYS MET ASP GLU SEQRES 47 A 690 ASP HIS ARG ALA ARG ALA PHE PHE PRO ASN MET VAL ASN SEQRES 48 A 690 MET ILE VAL LEU ASP LYS ASP LEU GLY ILE PRO LYS PRO SEQRES 49 A 690 PHE GLY PRO GLN VAL GLU GLU GLU CYS CYS LEU GLU MET SEQRES 50 A 690 HIS VAL ARG GLY LEU LEU GLU PRO LEU GLY LEU GLU CYS SEQRES 51 A 690 THR PHE ILE ASP ASP ILE SER ALA TYR HIS LYS PHE LEU SEQRES 52 A 690 GLY GLU VAL HIS CYS GLY THR ASN VAL ARG ARG LYS PRO SEQRES 53 A 690 PHE THR PHE LYS TRP TRP HIS MET VAL PRO SER ARG ARG SEQRES 54 A 690 SER HET MPD A 701 8 HET MPD A 702 8 HET MPD A 703 8 HET CA A 704 1 HET CA A 705 1 HET CA A 706 1 HET ACT A 707 4 HET ACT A 708 4 HET CA A 709 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION FORMUL 2 MPD 3(C6 H14 O2) FORMUL 5 CA 4(CA 2+) FORMUL 8 ACT 2(C2 H3 O2 1-) FORMUL 11 HOH *653(H2 O) HELIX 1 1 GLU A 165 ASP A 169 5 5 HELIX 2 2 SER A 174 LYS A 179 1 6 HELIX 3 3 MET A 206 ASP A 210 5 5 HELIX 4 4 ASN A 317 LYS A 330 1 14 HELIX 5 5 ARG A 347 GLU A 352 1 6 HELIX 6 6 THR A 403 GLY A 409 5 7 HELIX 7 7 THR A 444 GLN A 455 1 12 HELIX 8 8 HIS A 471 GLU A 474 5 4 HELIX 9 9 THR A 494 ASP A 507 1 14 HELIX 10 10 LEU A 518 ARG A 525 5 8 HELIX 11 11 THR A 527 SER A 533 1 7 HELIX 12 12 ASN A 534 GLY A 560 1 27 HELIX 13 13 THR A 562 GLN A 564 5 3 HELIX 14 14 CYS A 613 GLU A 623 1 11 HELIX 15 15 PRO A 624 GLY A 626 5 3 HELIX 16 16 ILE A 635 HIS A 639 5 5 HELIX 17 17 LYS A 659 MET A 663 5 5 SHEET 1 A 5 ARG A 3 THR A 6 0 SHEET 2 A 5 THR A 23 THR A 27 1 O TYR A 24 N ARG A 5 SHEET 3 A 5 THR A 75 THR A 80 -1 O LEU A 77 N THR A 27 SHEET 4 A 5 TRP A 49 ARG A 54 -1 N VAL A 53 O THR A 76 SHEET 5 A 5 GLU A 57 VAL A 61 -1 O GLU A 57 N ARG A 54 SHEET 1 B 5 VAL A 15 VAL A 20 0 SHEET 2 B 5 ASP A 107 ASP A 121 1 O GLY A 110 N VAL A 15 SHEET 3 B 5 ASP A 91 TYR A 98 -1 N VAL A 95 O ALA A 109 SHEET 4 B 5 THR A 39 HIS A 44 -1 N LYS A 43 O THR A 94 SHEET 5 B 5 TRP A 69 LEU A 70 -1 O TRP A 69 N PHE A 40 SHEET 1 C 6 VAL A 15 VAL A 20 0 SHEET 2 C 6 ASP A 107 ASP A 121 1 O GLY A 110 N VAL A 15 SHEET 3 C 6 SER A 182 GLY A 190 -1 O ARG A 187 N SER A 119 SHEET 4 C 6 GLY A 244 GLY A 254 -1 O PHE A 250 N MET A 184 SHEET 5 C 6 VAL A 212 GLU A 218 -1 N PHE A 215 O PHE A 251 SHEET 6 C 6 ARG A 225 LEU A 230 -1 O ILE A 227 N TYR A 216 SHEET 1 D 5 ALA A 149 LEU A 151 0 SHEET 2 D 5 THR A 283 ILE A 294 1 O ARG A 293 N LEU A 151 SHEET 3 D 5 LEU A 265 GLU A 274 -1 N VAL A 266 O PHE A 292 SHEET 4 D 5 TYR A 198 TYR A 203 -1 N GLU A 199 O LEU A 273 SHEET 5 D 5 TYR A 236 VAL A 239 -1 O VAL A 239 N ILE A 200 SHEET 1 E 4 ILE A 298 MET A 299 0 SHEET 2 E 4 ILE A 353 ALA A 360 -1 O TYR A 357 N ILE A 298 SHEET 3 E 4 LYS A 363 ASP A 370 -1 O LEU A 369 N ALA A 354 SHEET 4 E 4 GLY A 391 THR A 394 1 O GLY A 391 N VAL A 368 SHEET 1 F 3 GLU A 334 CYS A 338 0 SHEET 2 F 3 PRO A 306 CYS A 312 1 N VAL A 309 O GLU A 334 SHEET 3 F 3 GLY A 648 ARG A 653 -1 O ASN A 650 N PHE A 310 SHEET 1 G 3 LEU A 411 VAL A 413 0 SHEET 2 G 3 ILE A 429 SER A 433 -1 O LEU A 430 N GLU A 412 SHEET 3 G 3 VAL A 460 TYR A 463 1 O LEU A 462 N ILE A 431 SHEET 1 H 2 VAL A 417 VAL A 419 0 SHEET 2 H 2 LYS A 422 TYR A 424 -1 O LYS A 422 N VAL A 419 SHEET 1 I 3 MET A 476 PRO A 480 0 SHEET 2 I 3 PHE A 487 SER A 493 -1 O LEU A 490 N SER A 477 SHEET 3 I 3 ILE A 566 PRO A 570 1 O ILE A 567 N LEU A 489 SHEET 1 J 2 PHE A 573 MET A 575 0 SHEET 2 J 2 ALA A 581 ALA A 583 -1 O ARG A 582 N LYS A 574 SHEET 1 K 3 ILE A 592 LEU A 594 0 SHEET 2 K 3 ASP A 597 PRO A 601 -1 O ASP A 597 N LEU A 594 SHEET 3 K 3 GLU A 628 ILE A 632 1 O ILE A 632 N ILE A 600 SHEET 1 L 2 GLN A 607 VAL A 608 0 SHEET 2 L 2 GLU A 611 CYS A 612 -1 O GLU A 611 N VAL A 608 LINK OD1 ASP A 123 CA CA A 706 1555 1555 2.18 LINK OD1 ASP A 125 CA CA A 706 1555 1555 2.14 LINK OD1 ASP A 127 CA CA A 706 1555 1555 2.25 LINK O VAL A 129 CA CA A 706 1555 1555 2.23 LINK OE1 GLU A 131 CA CA A 706 1555 1555 2.28 LINK OD1 ASN A 154 CA CA A 705 1555 1555 2.31 LINK OD2 ASP A 156 CA CA A 704 1555 1555 2.34 LINK OD1 ASP A 156 CA CA A 705 1555 1555 2.33 LINK OE2 GLU A 158 CA CA A 704 1555 1555 2.57 LINK OE2 GLU A 158 CA CA A 705 1555 1555 2.39 LINK OD1 ASP A 166 CA CA A 705 1555 1555 2.26 LINK O ASP A 166 CA CA A 709 1555 1555 2.33 LINK OD1 ASP A 169 CA CA A 709 1555 1555 2.32 LINK O LYS A 171 CA CA A 709 1555 1555 2.29 LINK OD1 ASP A 177 CA CA A 705 1555 1555 2.36 LINK OD2 ASP A 180 CA CA A 704 1555 1555 2.38 LINK OD1 ASP A 180 CA CA A 704 1555 1555 2.60 LINK OD2 ASP A 180 CA CA A 705 1555 1555 2.23 LINK OD1 ASP A 389 CA CA A 704 1555 1555 2.31 LINK CA CA A 704 O HOH A 858 1555 1555 2.50 LINK CA CA A 704 O HOH A 878 1555 1555 2.40 LINK CA CA A 706 O HOH A1230 1555 1555 2.31 LINK CA CA A 709 O HOH A 823 1555 1555 2.49 LINK CA CA A 709 O HOH A 965 1555 1555 2.32 LINK CA CA A 709 O HOH A1110 1555 1555 2.40 LINK CA CA A 709 O HOH A1359 1555 1555 2.39 CISPEP 1 GLU A 400 SER A 401 0 -2.24 SITE 1 AC1 7 TYR A 216 GLU A 218 HIS A 237 VAL A 239 SITE 2 AC1 7 LYS A 240 PHE A 250 HOH A1320 SITE 1 AC2 7 SER A 433 SER A 434 PRO A 436 GLU A 461 SITE 2 AC2 7 LEU A 462 TRP A 550 HOH A1234 SITE 1 AC3 2 GLU A 199 HOH A1182 SITE 1 AC4 7 ASP A 156 GLU A 158 ASP A 180 ASP A 389 SITE 2 AC4 7 CA A 705 HOH A 858 HOH A 878 SITE 1 AC5 7 ASN A 154 ASP A 156 GLU A 158 ASP A 166 SITE 2 AC5 7 ASP A 177 ASP A 180 CA A 704 SITE 1 AC6 6 ASP A 123 ASP A 125 ASP A 127 VAL A 129 SITE 2 AC6 6 GLU A 131 HOH A1230 SITE 1 AC7 5 GLY A 12 SER A 13 ARG A 14 ASP A 107 SITE 2 AC7 5 GLN A 108 SITE 1 AC8 1 ILE A 280 SITE 1 AC9 7 ASP A 166 ASP A 169 LYS A 171 HOH A 823 SITE 2 AC9 7 HOH A 965 HOH A1110 HOH A1359 CRYST1 203.200 51.630 76.540 90.00 106.04 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 0.004921 0.000000 0.001415 0.00000 SCALE2 0.000000 0.019369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013594 0.00000