HEADER HYDROLASE 04-OCT-13 4N2C TITLE CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (F221/222A, 10 MM TITLE 2 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 4N2C 1 REMARK SEQADV LINK REVDAT 2 06-MAY-15 4N2C 1 JRNL REVDAT 1 04-FEB-15 4N2C 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. 3.02 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) : 3.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 13566 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 659 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 48.9618 - 5.1653 0.99 2964 165 0.2612 0.2770 REMARK 3 2 5.1653 - 4.1005 1.00 2907 159 0.2103 0.2437 REMARK 3 3 4.1005 - 3.5824 1.00 2924 137 0.2371 0.2676 REMARK 3 4 3.5824 - 3.2549 0.92 2644 126 0.2651 0.3113 REMARK 3 5 3.2549 - 3.0220 0.51 1468 72 0.3031 0.3135 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 : 0.29 REMARK 3 B_SOL : 5.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06440 REMARK 3 B22 (A**2) : -1.20320 REMARK 3 B33 (A**2) : 1.26760 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.06130 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 : 0.021 5142 REMARK 3 ANGLE : 0.959 7003 REMARK 3 CHIRALITY : 0.069 782 REMARK 3 PLANARITY : 0.004 904 REMARK 3 DIHEDRAL : 14.014 1842 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 203.5296 -0.3744 15.4932 REMARK 3 T TENSOR REMARK 3 T11: 0.2812 T22: 0.2408 REMARK 3 T33: 0.0414 T12: -0.0324 REMARK 3 T13: 0.0587 T23: 0.0932 REMARK 3 L TENSOR REMARK 3 L11: 6.5232 L22: 0.3637 REMARK 3 L33: 0.5198 L12: -0.3747 REMARK 3 L13: 1.1305 L23: 0.1389 REMARK 3 S TENSOR REMARK 3 S11: 0.0271 S12: -1.1014 S13: -0.0291 REMARK 3 S21: 0.0582 S22: -0.0122 S23: -0.0084 REMARK 3 S31: -0.0259 S32: -0.1459 S33: -0.0154 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 4N2C 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_1000082663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2836 REMARK 200 MONOCHROMATOR : SIDE SCATTERING I-BEAM BENT REMARK 200 SINGLE CRYSTAL, ASYMMETRIC CUT REMARK 200 4.9650 DEGREES REMARK 200 OPTICS : RH COATED FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : XDS, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13566 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.020 REMARK 200 RESOLUTION RANGE LOW (A) : 48.955 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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 4N25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, 10% ETHANOL, 50 MM MES, PH REMARK 280 5.6, 20 MM MAGNESIUM CHLORIDE, 1 MM SPERMIDINE, VAPOR DIFFUSION, REMARK 280 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 101.46500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 101.46500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.09000 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: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -146.0 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 405.86000 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 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 LEU A 2 REMARK 465 ASN A 317 REMARK 465 TYR A 318 REMARK 465 LEU A 319 REMARK 465 PHE A 320 REMARK 465 LEU A 321 REMARK 465 LYS A 322 REMARK 465 GLU A 323 REMARK 465 VAL A 324 REMARK 465 LYS A 325 REMARK 465 ASN A 326 REMARK 465 LEU A 327 REMARK 465 VAL A 328 REMARK 465 GLU A 329 REMARK 465 LYS A 330 REMARK 465 ILE A 635 REMARK 465 SER A 636 REMARK 465 ALA A 637 REMARK 465 TYR A 638 REMARK 465 SER A 666 REMARK 465 ARG A 667 REMARK 465 ARG A 668 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 ARG A 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 14 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CE NZ REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 GLU A 101 CG CD OE1 OE2 REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 TRP A 161 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 161 CZ3 CH2 REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 LYS A 179 CG CD CE NZ REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 225 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 MET A 314 CG SD CE REMARK 470 LEU A 335 CG CD1 CD2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 GLN A 340 CG CD OE1 NE2 REMARK 470 ARG A 344 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 383 CG CD CE NZ REMARK 470 GLU A 384 CG CD OE1 OE2 REMARK 470 LEU A 385 CG CD1 CD2 REMARK 470 LYS A 506 CG CD CE NZ REMARK 470 MET A 521 CG SD CE REMARK 470 LYS A 524 CG CD CE NZ REMARK 470 ARG A 525 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 530 CG CD CE NZ REMARK 470 ASP A 595 CG OD1 OD2 REMARK 470 GLU A 610 CG CD OE1 OE2 REMARK 470 PHE A 641 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 642 CG CD1 CD2 REMARK 470 LYS A 654 CG CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 483 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 316 N CA C O REMARK 480 SER A 495 CA CB OG REMARK 480 SER A 533 N CA C O CB OG 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 OE2 GLU A 131 CA CA A 706 1.45 REMARK 500 OE1 GLU A 253 O HOH A 834 1.74 REMARK 500 O PRO A 381 N LEU A 385 2.08 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 72 144.62 -177.28 REMARK 500 SER A 90 -4.97 86.92 REMARK 500 TYR A 173 -66.95 -109.57 REMARK 500 PRO A 191 -176.80 -68.69 REMARK 500 ALA A 221 -138.39 56.19 REMARK 500 ALA A 222 -127.53 43.35 REMARK 500 ARG A 233 -7.77 69.23 REMARK 500 MET A 276 -63.74 -94.78 REMARK 500 PRO A 284 75.78 -69.23 REMARK 500 PRO A 301 -177.80 -69.77 REMARK 500 VAL A 307 -64.11 -126.41 REMARK 500 MET A 314 -73.46 -135.13 REMARK 500 LYS A 315 71.97 59.80 REMARK 500 CYS A 333 160.56 179.73 REMARK 500 GLN A 340 -114.84 51.01 REMARK 500 LEU A 398 -64.24 -94.72 REMARK 500 GLN A 455 -9.77 66.02 REMARK 500 ALA A 458 72.74 43.06 REMARK 500 PRO A 482 63.38 -60.92 REMARK 500 LYS A 485 179.81 175.38 REMARK 500 LYS A 486 -17.62 78.10 REMARK 500 PHE A 487 -10.06 60.43 REMARK 500 LEU A 488 73.32 39.78 REMARK 500 LEU A 518 -125.25 57.98 REMARK 500 MET A 591 -179.75 -69.22 REMARK 500 ASP A 595 73.43 40.90 REMARK 500 LYS A 596 -134.20 60.63 REMARK 500 ASP A 597 72.02 43.54 REMARK 500 VAL A 645 -20.40 63.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 339 GLN A 340 149.07 REMARK 500 LYS A 486 PHE A 487 144.47 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 OD2 80.7 REMARK 620 3 ASP A 127 OD1 100.9 90.1 REMARK 620 4 VAL A 129 O 86.4 159.9 77.2 REMARK 620 5 GLU A 131 OE1 72.0 86.1 172.4 104.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 156 OD2 REMARK 620 2 GLU A 158 OE2 76.9 REMARK 620 3 ASP A 180 OD2 112.0 151.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 156 OD1 REMARK 620 2 ASP A 166 OD1 93.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 703 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 166 O REMARK 620 2 ASP A 169 OD1 74.2 REMARK 620 3 LYS A 171 O 148.0 73.8 REMARK 620 N 1 2 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 GLN A 350 OE1 REMARK 620 2 GLU A 354 OE1 112.6 REMARK 620 3 PHE A 408 O 96.8 95.3 REMARK 620 4 LEU A 411 O 172.0 74.3 78.0 REMARK 620 5 GLU A 412 OE2 94.2 144.4 104.7 81.4 REMARK 620 N 1 2 3 4 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 GLU A 352 OE2 REMARK 620 2 ASP A 370 OD1 78.8 REMARK 620 3 ASP A 370 OD2 119.2 45.6 REMARK 620 4 SER A 371 O 78.2 86.7 113.7 REMARK 620 5 ASP A 374 OD2 99.8 178.2 135.1 94.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA 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 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: 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 REMARK 900 RELATED ID: 4N2N RELATED DB: PDB DBREF 4N2C A 1 665 UNP Q9Y2J8 PADI2_HUMAN 1 665 SEQADV 4N2C MET A -20 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C GLY A -19 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -18 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -17 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -16 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -15 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -14 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -13 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -12 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -11 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -10 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -9 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C SER A -8 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C SER A -7 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C GLY A -6 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A -5 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C ILE A -4 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C GLU A -3 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C GLY A -2 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C ARG A -1 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C HIS A 0 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C ALA A 221 UNP Q9Y2J8 PHE 221 ENGINEERED MUTATION SEQADV 4N2C ALA A 222 UNP Q9Y2J8 PHE 222 ENGINEERED MUTATION SEQADV 4N2C SER A 666 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C ARG A 667 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C ARG A 668 UNP Q9Y2J8 EXPRESSION TAG SEQADV 4N2C 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 ALA ALA 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 GLU 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 CA A 701 1 HET CA A 702 1 HET CA A 703 1 HET CA A 704 1 HET CA A 705 1 HET CA A 706 1 HETNAM CA CALCIUM ION FORMUL 2 CA 6(CA 2+) FORMUL 8 HOH *36(H2 O) HELIX 1 1 ASN A 134 SER A 139 5 6 HELIX 2 2 GLU A 165 ASP A 169 5 5 HELIX 3 3 GLU A 176 MET A 181 1 6 HELIX 4 4 PHE A 339 ARG A 344 1 6 HELIX 5 5 THR A 403 SER A 407 5 5 HELIX 6 6 THR A 444 GLN A 455 1 12 HELIX 7 7 HIS A 471 PHE A 475 1 5 HELIX 8 8 THR A 494 ASP A 507 1 14 HELIX 9 9 THR A 527 SER A 533 1 7 HELIX 10 10 ASN A 534 GLY A 560 1 27 HELIX 11 11 THR A 562 GLN A 564 5 3 HELIX 12 12 CYS A 613 GLU A 623 1 11 HELIX 13 13 LYS A 659 MET A 663 5 5 SHEET 1 A 5 GLU A 4 ARG A 8 0 SHEET 2 A 5 TYR A 24 ASP A 28 1 O TRP A 26 N VAL A 7 SHEET 3 A 5 THR A 75 MET A 81 -1 O VAL A 79 N LEU A 25 SHEET 4 A 5 VAL A 48 ARG A 54 -1 N TRP A 49 O THR A 80 SHEET 5 A 5 GLU A 57 VAL A 61 -1 O VAL A 61 N VAL A 50 SHEET 1 B 5 ARG A 14 VAL A 20 0 SHEET 2 B 5 GLN A 108 ASP A 121 1 O PHE A 112 N ALA A 17 SHEET 3 B 5 ASP A 91 TYR A 98 -1 N ASP A 91 O LEU A 113 SHEET 4 B 5 THR A 39 HIS A 44 -1 N THR A 39 O TYR A 98 SHEET 5 B 5 TRP A 69 LEU A 70 -1 O TRP A 69 N PHE A 40 SHEET 1 C 6 ARG A 14 VAL A 20 0 SHEET 2 C 6 GLN A 108 ASP A 121 1 O PHE A 112 N ALA A 17 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 ALA A 246 N THR A 188 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 HIS A 237 N LEU A 202 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 LYS A 363 N ALA A 360 SHEET 4 E 4 GLY A 391 THR A 394 1 O GLY A 391 N PRO A 366 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 311 O CYS A 338 SHEET 3 F 3 THR A 649 ARG A 653 -1 O ARG A 652 N SER A 308 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 VAL A 460 N ILE A 429 SHEET 1 H 2 VAL A 417 VAL A 419 0 SHEET 2 H 2 LYS A 422 TYR A 424 -1 O TYR A 424 N VAL A 417 SHEET 1 I 3 MET A 476 SER A 477 0 SHEET 2 I 3 LEU A 489 SER A 493 -1 O LEU A 490 N SER A 477 SHEET 3 I 3 ILE A 566 PRO A 570 1 O LEU A 569 N MET A 491 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 2 GLN A 607 VAL A 608 0 SHEET 2 K 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 2.31 LINK OD2 ASP A 125 CA CA A 706 1555 1555 2.15 LINK OD1 ASP A 127 CA CA A 706 1555 1555 2.67 LINK O VAL A 129 CA CA A 706 1555 1555 2.49 LINK OE1 GLU A 131 CA CA A 706 1555 1555 3.07 LINK OD2 ASP A 156 CA CA A 701 1555 1555 2.57 LINK OD1 ASP A 156 CA CA A 702 1555 1555 2.82 LINK OE2 GLU A 158 CA CA A 701 1555 1555 2.97 LINK OD1 ASP A 166 CA CA A 702 1555 1555 2.36 LINK O ASP A 166 CA CA A 703 1555 1555 2.53 LINK OD1 ASP A 169 CA CA A 703 1555 1555 2.33 LINK O LYS A 171 CA CA A 703 1555 1555 2.50 LINK OD2 ASP A 180 CA CA A 701 1555 1555 3.01 LINK OE1 GLN A 350 CA CA A 704 1555 1555 2.44 LINK OE2 GLU A 352 CA CA A 705 1555 1555 2.68 LINK OE1 GLU A 354 CA CA A 704 1555 1555 2.78 LINK OD1 ASP A 370 CA CA A 705 1555 1555 2.68 LINK OD2 ASP A 370 CA CA A 705 1555 1555 2.96 LINK O SER A 371 CA CA A 705 1555 1555 2.33 LINK OD2 ASP A 374 CA CA A 705 1555 1555 2.66 LINK O PHE A 408 CA CA A 704 1555 1555 2.13 LINK O LEU A 411 CA CA A 704 1555 1555 2.41 LINK OE2 GLU A 412 CA CA A 704 1555 1555 2.96 CISPEP 1 CYS A 313 MET A 314 0 -24.93 CISPEP 2 LYS A 315 ASP A 316 0 6.86 CISPEP 3 LYS A 383 GLU A 384 0 2.10 CISPEP 4 GLY A 483 THR A 484 0 1.39 CISPEP 5 GLY A 519 GLY A 520 0 5.70 CISPEP 6 GLY A 520 MET A 521 0 1.49 CISPEP 7 PHE A 641 LEU A 642 0 3.37 SITE 1 AC1 4 ASP A 156 GLU A 158 ASP A 180 ASP A 389 SITE 1 AC2 6 ASN A 154 ASP A 156 GLU A 158 ASP A 166 SITE 2 AC2 6 ASP A 177 ASP A 180 SITE 1 AC3 3 ASP A 166 ASP A 169 LYS A 171 SITE 1 AC4 5 GLN A 350 GLU A 354 PHE A 408 LEU A 411 SITE 2 AC4 5 GLU A 412 SITE 1 AC5 4 GLU A 352 ASP A 370 SER A 371 ASP A 374 SITE 1 AC6 5 ASP A 123 ASP A 125 ASP A 127 VAL A 129 SITE 2 AC6 5 GLU A 131 CRYST1 202.930 52.180 75.820 90.00 105.21 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 0.004928 0.000000 0.001340 0.00000 SCALE2 0.000000 0.019164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013668 0.00000