HEADER LYASE 21-SEP-15 5DVX TITLE CRYSTAL STRUCTURE OF THE CATALYTIC-DOMAIN OF HUMAN CARBONIC ANHYDRASE TITLE 2 IX AT 1.6 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC-DOMAIN (UNP RESIDUES 140-399); COMPND 5 SYNONYM: CARBONATE DEHYDRATASE IX,CARBONIC ANHYDRASE IX,CAIX,MEMBRANE COMPND 6 ANTIGEN MN,P54/58N,RENAL CELL CARCINOMA-ASSOCIATED ANTIGEN G250,RCC- COMPND 7 ASSOCIATED ANTIGEN G250,PMW1; COMPND 8 EC: 4.2.1.1; COMPND 9 ENGINEERED: YES; COMPND 10 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: CA9, G250, MN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CARBONIC ANHYDRASE IX, CATALYTIC DOMAIN, WATER NETWORK, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR B.P.MAHON,L.SOCORRO,J.M.DRISCOLL,R.MCKENNA REVDAT 7 30-OCT-24 5DVX 1 REMARK REVDAT 6 27-SEP-23 5DVX 1 REMARK LINK REVDAT 5 04-DEC-19 5DVX 1 REMARK REVDAT 4 27-SEP-17 5DVX 1 JRNL REMARK REVDAT 3 07-SEP-16 5DVX 1 JRNL REVDAT 2 17-AUG-16 5DVX 1 JRNL REVDAT 1 03-AUG-16 5DVX 0 JRNL AUTH B.P.MAHON,A.BHATT,L.SOCORRO,J.M.DRISCOLL,C.OKOH, JRNL AUTH 2 C.L.LOMELINO,M.Y.MBOGE,J.J.KURIAN,C.TU,M.AGBANDJE-MCKENNA, JRNL AUTH 3 S.C.FROST,R.MCKENNA JRNL TITL THE STRUCTURE OF CARBONIC ANHYDRASE IX IS ADAPTED FOR LOW-PH JRNL TITL 2 CATALYSIS. JRNL REF BIOCHEMISTRY V. 55 4642 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27439028 JRNL DOI 10.1021/ACS.BIOCHEM.6B00243 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1839 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 77844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.320 REMARK 3 FREE R VALUE TEST SET COUNT : 3607 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 19.8368 - 4.7125 0.99 6196 145 0.1572 0.1492 REMARK 3 2 4.7125 - 3.7487 1.00 6272 142 0.1311 0.1444 REMARK 3 3 3.7487 - 3.2773 1.00 6239 149 0.1506 0.1832 REMARK 3 4 3.2773 - 2.9787 1.00 6260 155 0.1631 0.1765 REMARK 3 5 2.9787 - 2.7658 1.00 6202 147 0.1693 0.1987 REMARK 3 6 2.7658 - 2.6031 1.00 6262 166 0.1650 0.1741 REMARK 3 7 2.6031 - 2.4730 1.00 6229 148 0.1645 0.2026 REMARK 3 8 2.4730 - 2.3656 1.00 6266 159 0.1693 0.2121 REMARK 3 9 2.3656 - 2.2746 1.00 6233 144 0.1721 0.1909 REMARK 3 10 2.2746 - 2.1962 1.00 6253 153 0.1767 0.2484 REMARK 3 11 2.1962 - 2.1276 1.00 6253 143 0.1829 0.2391 REMARK 3 12 2.1276 - 2.0669 1.00 6216 152 0.1752 0.1807 REMARK 3 13 2.0669 - 2.0125 1.00 6240 143 0.1769 0.2183 REMARK 3 14 2.0125 - 1.9635 1.00 6290 145 0.1762 0.2109 REMARK 3 15 1.9635 - 1.9189 1.00 6256 158 0.1889 0.1801 REMARK 3 16 1.9189 - 1.8781 0.99 6213 122 0.1928 0.2003 REMARK 3 17 1.8781 - 1.8405 0.99 6168 156 0.1910 0.2232 REMARK 3 18 1.8405 - 1.8058 0.97 6001 152 0.1810 0.2144 REMARK 3 19 1.8058 - 1.7736 0.95 6014 125 0.1820 0.1880 REMARK 3 20 1.7736 - 1.7435 0.92 5691 144 0.1824 0.2361 REMARK 3 21 1.7435 - 1.7154 0.87 5449 134 0.1876 0.2190 REMARK 3 22 1.7154 - 1.6891 0.83 5162 107 0.1901 0.2170 REMARK 3 23 1.6891 - 1.6642 0.78 4902 121 0.1964 0.2010 REMARK 3 24 1.6642 - 1.6408 0.73 4536 114 0.1952 0.2259 REMARK 3 25 1.6408 - 1.6186 0.71 4450 98 0.1969 0.2000 REMARK 3 26 1.6186 - 1.5976 0.61 3827 85 0.2070 0.2348 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.88 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 : 0.007 4324 REMARK 3 ANGLE : 1.151 5897 REMARK 3 CHIRALITY : 0.047 641 REMARK 3 PLANARITY : 0.006 777 REMARK 3 DIHEDRAL : 15.337 1644 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): 2.0796 3.4303 -6.2038 REMARK 3 T TENSOR REMARK 3 T11: 0.0689 T22: 0.0632 REMARK 3 T33: 0.0775 T12: -0.0000 REMARK 3 T13: -0.0111 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.0381 L22: 0.0295 REMARK 3 L33: 0.7488 L12: -0.0120 REMARK 3 L13: 0.0289 L23: -0.2685 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0280 S13: 0.0043 REMARK 3 S21: 0.0472 S22: -0.0303 S23: -0.0048 REMARK 3 S31: -0.1097 S32: 0.0061 S33: -0.0350 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 5DVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9177 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86682 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3IAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS HCL, PH 8.5, 8% (W/V) PEG REMARK 280 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 28.93850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.48200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.37200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.48200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.93850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.37200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 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 HIS B 140 REMARK 465 SER B 396 REMARK 465 SER B 397 REMARK 465 PRO B 398 REMARK 465 ARG B 399 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 NH2 ARG A 221 O HOH A 501 1.25 REMARK 500 N HIS A 140 O HOH A 502 1.58 REMARK 500 OE1 GLU B 242 O HOH B 501 2.06 REMARK 500 CD ARG A 221 O HOH A 515 2.12 REMARK 500 OE1 GLU B 192 O HOH B 502 2.12 REMARK 500 NH2 ARG A 295 O HOH A 503 2.16 REMARK 500 NE2 HIS A 140 O HOH A 504 2.17 REMARK 500 NH2 ARG A 194 OE2 GLU A 305 2.17 REMARK 500 OD2 ASP B 146 O HOH B 503 2.17 REMARK 500 OE2 GLU A 285 O HOH A 505 2.18 REMARK 500 O HOH B 502 O HOH B 684 2.19 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 HIS A 140 CB GLU B 242 2555 1.41 REMARK 500 O HIS A 140 CB GLU B 242 2555 1.46 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 HIS A 140 CG HIS A 140 CD2 0.102 REMARK 500 HIS A 140 CG HIS A 140 CD2 0.102 REMARK 500 HIS A 140 CG HIS A 140 ND1 -0.129 REMARK 500 HIS A 140 CG HIS A 140 ND1 -0.128 REMARK 500 HIS A 140 C HIS A 140 O 0.161 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 391 -168.30 -75.77 REMARK 500 ALA A 392 -86.13 -67.47 REMARK 500 ALA B 232 108.38 -8.64 REMARK 500 ALA B 232 108.38 -55.58 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 HIS A 140 TRP A 141 -91.31 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 140 ND1 REMARK 620 2 TRP A 141 N 96.3 REMARK 620 3 TRP A 141 O 168.2 77.7 REMARK 620 4 HIS A 200 NE2 93.4 147.3 86.8 REMARK 620 5 HIS B 244 NE2 136.3 84.5 33.9 67.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 226 NE2 REMARK 620 2 HIS A 228 NE2 105.0 REMARK 620 3 HIS A 251 ND1 113.8 97.2 REMARK 620 4 HOH A 606 O 106.5 115.3 118.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 409 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 244 NE2 REMARK 620 2 TRP B 141 N 108.0 REMARK 620 3 TRP B 141 O 101.6 76.8 REMARK 620 4 HIS B 200 NE2 103.8 147.1 88.8 REMARK 620 5 HOH B 671 O 91.9 89.8 163.3 97.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 226 NE2 REMARK 620 2 HIS B 228 NE2 105.5 REMARK 620 3 HIS B 251 ND1 114.9 98.3 REMARK 620 4 HOH B 575 O 103.9 114.1 119.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 405 DBREF 5DVX A 140 399 UNP Q16790 CAH9_HUMAN 140 399 DBREF 5DVX B 140 399 UNP Q16790 CAH9_HUMAN 140 399 SEQADV 5DVX SER A 174 UNP Q16790 CYS 174 ENGINEERED MUTATION SEQADV 5DVX SER A 183 UNP Q16790 LEU 183 ENGINEERED MUTATION SEQADV 5DVX LYS A 213 UNP Q16790 ALA 213 ENGINEERED MUTATION SEQADV 5DVX LYS A 258 UNP Q16790 ALA 258 ENGINEERED MUTATION SEQADV 5DVX TYR A 259 UNP Q16790 PHE 259 ENGINEERED MUTATION SEQADV 5DVX SER A 350 UNP Q16790 MET 350 ENGINEERED MUTATION SEQADV 5DVX SER B 174 UNP Q16790 CYS 174 ENGINEERED MUTATION SEQADV 5DVX SER B 183 UNP Q16790 LEU 183 ENGINEERED MUTATION SEQADV 5DVX LYS B 213 UNP Q16790 ALA 213 ENGINEERED MUTATION SEQADV 5DVX LYS B 258 UNP Q16790 ALA 258 ENGINEERED MUTATION SEQADV 5DVX TYR B 259 UNP Q16790 PHE 259 ENGINEERED MUTATION SEQADV 5DVX SER B 350 UNP Q16790 MET 350 ENGINEERED MUTATION SEQRES 1 A 260 HIS TRP ARG TYR GLY GLY ASP PRO PRO TRP PRO ARG VAL SEQRES 2 A 260 SER PRO ALA CYS ALA GLY ARG PHE GLN SER PRO VAL ASP SEQRES 3 A 260 ILE ARG PRO GLN LEU ALA ALA PHE SER PRO ALA LEU ARG SEQRES 4 A 260 PRO LEU GLU LEU SER GLY PHE GLN LEU PRO PRO LEU PRO SEQRES 5 A 260 GLU LEU ARG LEU ARG ASN ASN GLY HIS SER VAL GLN LEU SEQRES 6 A 260 THR LEU PRO PRO GLY LEU GLU MET LYS LEU GLY PRO GLY SEQRES 7 A 260 ARG GLU TYR ARG ALA LEU GLN LEU HIS LEU HIS TRP GLY SEQRES 8 A 260 ALA ALA GLY ARG PRO GLY SER GLU HIS THR VAL GLU GLY SEQRES 9 A 260 HIS ARG PHE PRO ALA GLU ILE HIS VAL VAL HIS LEU SER SEQRES 10 A 260 THR LYS TYR ALA ARG VAL ASP GLU ALA LEU GLY ARG PRO SEQRES 11 A 260 GLY GLY LEU ALA VAL LEU ALA ALA PHE LEU GLU GLU GLY SEQRES 12 A 260 PRO GLU GLU ASN SER ALA TYR GLU GLN LEU LEU SER ARG SEQRES 13 A 260 LEU GLU GLU ILE ALA GLU GLU GLY SER GLU THR GLN VAL SEQRES 14 A 260 PRO GLY LEU ASP ILE SER ALA LEU LEU PRO SER ASP PHE SEQRES 15 A 260 SER ARG TYR PHE GLN TYR GLU GLY SER LEU THR THR PRO SEQRES 16 A 260 PRO CYS ALA GLN GLY VAL ILE TRP THR VAL PHE ASN GLN SEQRES 17 A 260 THR VAL SER LEU SER ALA LYS GLN LEU HIS THR LEU SER SEQRES 18 A 260 ASP THR LEU TRP GLY PRO GLY ASP SER ARG LEU GLN LEU SEQRES 19 A 260 ASN PHE ARG ALA THR GLN PRO LEU ASN GLY ARG VAL ILE SEQRES 20 A 260 GLU ALA SER PHE PRO ALA GLY VAL ASP SER SER PRO ARG SEQRES 1 B 260 HIS TRP ARG TYR GLY GLY ASP PRO PRO TRP PRO ARG VAL SEQRES 2 B 260 SER PRO ALA CYS ALA GLY ARG PHE GLN SER PRO VAL ASP SEQRES 3 B 260 ILE ARG PRO GLN LEU ALA ALA PHE SER PRO ALA LEU ARG SEQRES 4 B 260 PRO LEU GLU LEU SER GLY PHE GLN LEU PRO PRO LEU PRO SEQRES 5 B 260 GLU LEU ARG LEU ARG ASN ASN GLY HIS SER VAL GLN LEU SEQRES 6 B 260 THR LEU PRO PRO GLY LEU GLU MET LYS LEU GLY PRO GLY SEQRES 7 B 260 ARG GLU TYR ARG ALA LEU GLN LEU HIS LEU HIS TRP GLY SEQRES 8 B 260 ALA ALA GLY ARG PRO GLY SER GLU HIS THR VAL GLU GLY SEQRES 9 B 260 HIS ARG PHE PRO ALA GLU ILE HIS VAL VAL HIS LEU SER SEQRES 10 B 260 THR LYS TYR ALA ARG VAL ASP GLU ALA LEU GLY ARG PRO SEQRES 11 B 260 GLY GLY LEU ALA VAL LEU ALA ALA PHE LEU GLU GLU GLY SEQRES 12 B 260 PRO GLU GLU ASN SER ALA TYR GLU GLN LEU LEU SER ARG SEQRES 13 B 260 LEU GLU GLU ILE ALA GLU GLU GLY SER GLU THR GLN VAL SEQRES 14 B 260 PRO GLY LEU ASP ILE SER ALA LEU LEU PRO SER ASP PHE SEQRES 15 B 260 SER ARG TYR PHE GLN TYR GLU GLY SER LEU THR THR PRO SEQRES 16 B 260 PRO CYS ALA GLN GLY VAL ILE TRP THR VAL PHE ASN GLN SEQRES 17 B 260 THR VAL SER LEU SER ALA LYS GLN LEU HIS THR LEU SER SEQRES 18 B 260 ASP THR LEU TRP GLY PRO GLY ASP SER ARG LEU GLN LEU SEQRES 19 B 260 ASN PHE ARG ALA THR GLN PRO LEU ASN GLY ARG VAL ILE SEQRES 20 B 260 GLU ALA SER PHE PRO ALA GLY VAL ASP SER SER PRO ARG HET ZN A 401 1 HET ZN A 402 1 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET CL A 406 1 HET CL A 407 1 HET TRS A 408 8 HET ZN A 409 1 HET ZN B 401 1 HET GOL B 402 6 HET GOL B 403 6 HET GOL B 404 6 HET CL B 405 1 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 3 ZN 4(ZN 2+) FORMUL 5 GOL 6(C3 H8 O3) FORMUL 8 CL 3(CL 1-) FORMUL 10 TRS C4 H12 N O3 1+ FORMUL 17 HOH *626(H2 O) HELIX 1 AA1 PRO A 148 SER A 153 1 6 HELIX 2 AA2 PRO A 154 GLY A 158 5 5 HELIX 3 AA3 ARG A 167 ALA A 171 5 5 HELIX 4 AA4 ARG A 261 LEU A 266 1 6 HELIX 5 AA5 ASN A 286 SER A 294 1 9 HELIX 6 AA6 ARG A 295 ALA A 300 5 6 HELIX 7 AA7 ASP A 312 LEU A 317 5 6 HELIX 8 AA8 SER A 352 THR A 362 1 11 HELIX 9 AA9 PRO B 148 VAL B 152 5 5 HELIX 10 AB1 SER B 153 GLY B 158 5 6 HELIX 11 AB2 ARG B 167 ALA B 171 5 5 HELIX 12 AB3 ARG B 261 LEU B 266 1 6 HELIX 13 AB4 ASN B 286 SER B 294 1 9 HELIX 14 AB5 ARG B 295 ALA B 300 5 6 HELIX 15 AB6 ASP B 312 LEU B 317 5 6 HELIX 16 AB7 SER B 352 THR B 362 1 11 SHEET 1 AA1 2 ASP A 165 ILE A 166 0 SHEET 2 AA1 2 THR A 240 VAL A 241 1 O THR A 240 N ILE A 166 SHEET 1 AA210 ALA A 172 PHE A 173 0 SHEET 2 AA210 GLU A 387 ALA A 388 1 O ALA A 388 N ALA A 172 SHEET 3 AA210 TYR A 324 SER A 330 -1 N GLN A 326 O GLU A 387 SHEET 4 AA210 GLN A 338 PHE A 345 -1 O VAL A 340 N GLY A 329 SHEET 5 AA210 LEU A 272 GLU A 281 1 N ALA A 276 O THR A 343 SHEET 6 AA210 ALA A 248 SER A 256 -1 N HIS A 254 O ALA A 273 SHEET 7 AA210 ARG A 218 TRP A 229 -1 N LEU A 223 O VAL A 253 SHEET 8 AA210 VAL A 202 THR A 205 -1 N LEU A 204 O LEU A 225 SHEET 9 AA210 LEU A 193 ASN A 197 -1 N ARG A 196 O GLN A 203 SHEET 10 AA210 GLU A 305 VAL A 308 -1 O THR A 306 N LEU A 195 SHEET 1 AA3 6 GLU A 181 SER A 183 0 SHEET 2 AA3 6 GLU A 211 GLY A 215 -1 O LYS A 213 N GLU A 181 SHEET 3 AA3 6 ARG A 218 TRP A 229 -1 O ARG A 218 N LEU A 214 SHEET 4 AA3 6 ALA A 248 SER A 256 -1 O VAL A 253 N LEU A 223 SHEET 5 AA3 6 LEU A 272 GLU A 281 -1 O ALA A 273 N HIS A 254 SHEET 6 AA3 6 VAL A 349 LEU A 351 1 O VAL A 349 N GLU A 280 SHEET 1 AA4 2 ASP B 165 ILE B 166 0 SHEET 2 AA4 2 THR B 240 VAL B 241 1 O THR B 240 N ILE B 166 SHEET 1 AA510 ALA B 172 PHE B 173 0 SHEET 2 AA510 GLU B 387 ALA B 388 1 O ALA B 388 N ALA B 172 SHEET 3 AA510 TYR B 324 SER B 330 -1 N GLN B 326 O GLU B 387 SHEET 4 AA510 GLN B 338 PHE B 345 -1 O VAL B 340 N GLY B 329 SHEET 5 AA510 LEU B 272 GLU B 281 1 N ALA B 276 O THR B 343 SHEET 6 AA510 ALA B 248 SER B 256 -1 N HIS B 254 O ALA B 273 SHEET 7 AA510 ARG B 218 TRP B 229 -1 N LEU B 223 O VAL B 253 SHEET 8 AA510 VAL B 202 THR B 205 -1 N LEU B 204 O LEU B 225 SHEET 9 AA510 LEU B 193 ASN B 197 -1 N ARG B 196 O GLN B 203 SHEET 10 AA510 GLU B 305 VAL B 308 -1 O VAL B 308 N LEU B 193 SHEET 1 AA6 6 GLU B 181 SER B 183 0 SHEET 2 AA6 6 GLU B 211 GLY B 215 -1 O LYS B 213 N GLU B 181 SHEET 3 AA6 6 ARG B 218 TRP B 229 -1 O TYR B 220 N MET B 212 SHEET 4 AA6 6 ALA B 248 SER B 256 -1 O VAL B 253 N LEU B 223 SHEET 5 AA6 6 LEU B 272 GLU B 281 -1 O ALA B 273 N HIS B 254 SHEET 6 AA6 6 VAL B 349 LEU B 351 1 O VAL B 349 N GLU B 280 SSBOND 1 CYS A 156 CYS A 336 1555 1555 2.05 SSBOND 2 CYS B 156 CYS B 336 1555 1555 2.05 LINK ND1AHIS A 140 ZN ZN A 402 1555 1555 2.05 LINK N TRP A 141 ZN ZN A 402 1555 1555 2.16 LINK O TRP A 141 ZN ZN A 402 1555 1555 2.31 LINK NE2 HIS A 200 ZN ZN A 402 1555 1555 2.07 LINK NE2 HIS A 226 ZN ZN A 401 1555 1555 2.03 LINK NE2 HIS A 228 ZN ZN A 401 1555 1555 2.08 LINK NE2 HIS A 244 ZN ZN A 409 1555 1555 2.06 LINK ND1 HIS A 251 ZN ZN A 401 1555 1555 2.05 LINK ZN ZN A 401 O HOH A 606 1555 1555 1.94 LINK ZN ZN A 402 NE2 HIS B 244 2554 1555 2.09 LINK ZN ZN A 409 N TRP B 141 1555 1555 2.06 LINK ZN ZN A 409 O TRP B 141 1555 1555 2.27 LINK ZN ZN A 409 NE2 HIS B 200 1555 1555 2.07 LINK ZN ZN A 409 O HOH B 671 1555 1555 2.12 LINK NE2 HIS B 226 ZN ZN B 401 1555 1555 2.04 LINK NE2 HIS B 228 ZN ZN B 401 1555 1555 2.06 LINK ND1 HIS B 251 ZN ZN B 401 1555 1555 2.04 LINK ZN ZN B 401 O HOH B 575 1555 1555 1.92 CISPEP 1 ASP A 146 PRO A 147 0 -2.79 CISPEP 2 SER A 162 PRO A 163 0 -0.30 CISPEP 3 LEU A 190 PRO A 191 0 2.79 CISPEP 4 PRO A 334 PRO A 335 0 13.03 CISPEP 5 ASP B 146 PRO B 147 0 -1.02 CISPEP 6 SER B 162 PRO B 163 0 0.45 CISPEP 7 LEU B 190 PRO B 191 0 2.29 CISPEP 8 PRO B 334 PRO B 335 0 13.03 SITE 1 AC1 4 HIS A 226 HIS A 228 HIS A 251 HOH A 606 SITE 1 AC2 4 HIS A 140 TRP A 141 HIS A 200 HIS B 244 SITE 1 AC3 4 GLN A 224 HOH A 506 HOH A 638 HOH A 755 SITE 1 AC4 8 ARG A 151 GLN A 326 TYR A 327 GLU A 328 SITE 2 AC4 8 ILE A 341 HOH A 512 HOH A 538 HOH A 595 SITE 1 AC5 8 ARG A 151 VAL A 152 GLU A 387 HOH A 521 SITE 2 AC5 8 HOH A 646 GLY B 393 VAL B 394 ASP B 395 SITE 1 AC6 2 ARG A 159 GLN A 338 SITE 1 AC7 2 GLU A 242 HOH A 579 SITE 1 AC8 5 LEU A 373 PHE A 375 HOH A 575 HOH A 611 SITE 2 AC8 5 HOH A 675 SITE 1 AC9 4 HIS A 244 TRP B 141 HIS B 200 HOH B 671 SITE 1 AD1 4 HIS B 226 HIS B 228 HIS B 251 HOH B 575 SITE 1 AD2 6 GLN B 224 VAL B 253 HOH B 586 HOH B 602 SITE 2 AD2 6 HOH B 611 HOH B 683 SITE 1 AD3 4 PRO B 269 GLY B 270 GLU B 328 HOH B 511 SITE 1 AD4 6 PRO A 208 PHE B 160 ARG B 384 HOH B 514 SITE 2 AD4 6 HOH B 547 HOH B 707 SITE 1 AD5 2 ARG B 159 GLN B 338 CRYST1 57.877 102.744 108.964 90.00 90.00 90.00 P 21 21 21 8 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 0.017278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009177 0.00000