HEADER PROTEIN BINDING 23-DEC-14 4XED TITLE PKD DOMAIN OF M14-LIKE PEPTIDASE FROM THERMOPLASMATALES ARCHAEON SCGC TITLE 2 AB-540-F20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE M14, CARBOXYPEPTIDASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PKD DOMAIN RESIDUES 667-762; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMATALES ARCHAEON SCGC AB-540-F20; SOURCE 3 ORGANISM_TAXID: 1242866; SOURCE 4 GENE: MBGDF03_00742; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PGROW7-K; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG68 KEYWDS SINGLE CELL GENOMICS, MARINE SEDIMENT, STRUCTURAL GENOMICS, PSI- KEYWDS 2 BIOLOGY, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, PROTEIN KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.MICHALSKA,G.JOACHIMIAK,M.ENDRES,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 3 25-DEC-19 4XED 1 REMARK REVDAT 2 20-SEP-17 4XED 1 SOURCE KEYWDS REMARK REVDAT 1 13-MAY-15 4XED 0 JRNL AUTH K.MICHALSKA,G.JOACHIMIAK,M.ENDRES,A.JOACHIMIAK, JRNL AUTH 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) JRNL TITL PKD DOMAIN OF M14-LIKE PEPTIDASE FROM THERMOPLASMATALES JRNL TITL 2 ARCHAEON SCGC AB-540-F20 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 25851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 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 19.9068 - 2.4536 0.99 3260 140 0.1441 0.1583 REMARK 3 2 2.4536 - 1.9480 1.00 3199 135 0.1208 0.1490 REMARK 3 3 1.9480 - 1.7019 1.00 3152 136 0.1148 0.1495 REMARK 3 4 1.7019 - 1.5464 1.00 3127 133 0.1302 0.1653 REMARK 3 5 1.5464 - 1.4356 1.00 3119 120 0.1402 0.1949 REMARK 3 6 1.4356 - 1.3510 0.99 3107 139 0.1583 0.2044 REMARK 3 7 1.3510 - 1.2833 0.98 3026 143 0.1763 0.2587 REMARK 3 8 1.2833 - 1.2300 0.90 2803 112 0.1747 0.1950 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.480 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 : 0.012 863 REMARK 3 ANGLE : 1.435 1187 REMARK 3 CHIRALITY : 0.087 124 REMARK 3 PLANARITY : 0.009 157 REMARK 3 DIHEDRAL : 12.940 307 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: HYDROGEN ATOMS HAVE BEEN ADDED REMARK 3 IN RIDING POSITIONS, UNMODELED DENSITY NEAR THR89 POSSIBLY REMARK 3 CORRESPONDS TO CALCIUM ION BUT DUE TO INCOMPLETE AND REMARK 3 INCOSISTENT COORDINATION IT COULD NOT BE MODELED WITH REMARK 3 CONFIDENCE. REMARK 4 REMARK 4 4XED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25859 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, SHELX, MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CA ACETATE, 0.1 M NA REMARK 280 ACETATE/ACETIC ACID PH 4.5, 30% PEG 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.09300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.43450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.25450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.09300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.43450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.25450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.09300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 24.43450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.25450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.09300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 24.43450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.25450 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 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 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 A 283 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 304 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 SER A -2 REMARK 465 ASN A -1 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 304 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 305 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 310 DISTANCE = 6.04 ANGSTROMS 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 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 1 OD1 REMARK 620 2 ASP A 2 O 88.7 REMARK 620 3 ASP A 29 OD1 138.6 114.9 REMARK 620 4 ASP A 29 OD2 168.8 89.3 51.5 REMARK 620 5 ASN A 31 OD1 72.3 81.0 78.2 118.2 REMARK 620 6 ASP A 33 OD2 80.2 168.4 76.1 100.9 98.7 REMARK 620 7 ASP A 79 OD2 80.7 85.7 131.7 88.2 150.1 89.1 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 CA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MCSG-APC111705 RELATED DB: TARGETTRACK DBREF 4XED A 1 96 UNP M7U057 M7U057_9EURY 667 762 SEQADV 4XED SER A -2 UNP M7U057 EXPRESSION TAG SEQADV 4XED ASN A -1 UNP M7U057 EXPRESSION TAG SEQADV 4XED ALA A 0 UNP M7U057 EXPRESSION TAG SEQRES 1 A 99 SER ASN ALA ASN ASP PRO PRO ASN ILE PRO ASN VAL THR SEQRES 2 A 99 GLY PRO THR ASN GLY ASN ILE GLY THR THR TYR ASN TYR SEQRES 3 A 99 THR PHE VAL THR THR ASP PRO ASN GLY ASP ASN ILE THR SEQRES 4 A 99 TYR TYR ILE GLU TRP GLY ASP GLY PHE THR GLU GLU TRP SEQRES 5 A 99 ILE GLY PRO TYR ALA SER GLY GLU GLU VAL ILE PHE SER SEQRES 6 A 99 HIS THR TRP ASP LYS LYS GLY THR TYR VAL VAL ARG ALA SEQRES 7 A 99 LYS ALA LYS ASP ILE LEU ASN TYR GLU SER SER TRP GLY SEQRES 8 A 99 THR LEU GLU VAL THR MSE PRO LYS MODRES 4XED MSE A 94 MET MODIFIED RESIDUE HET MSE A 94 8 HET CA A 101 1 HET EDO A 102 4 HET EDO A 103 4 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 CA CA 2+ FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *123(H2 O) SHEET 1 AA1 3 ASN A 8 THR A 10 0 SHEET 2 AA1 3 TYR A 21 VAL A 26 -1 O THR A 24 N THR A 10 SHEET 3 AA1 3 VAL A 59 HIS A 63 -1 O VAL A 59 N PHE A 25 SHEET 1 AA2 4 THR A 46 TYR A 53 0 SHEET 2 AA2 4 ILE A 35 GLU A 40 -1 N ILE A 35 O TYR A 53 SHEET 3 AA2 4 GLY A 69 ASP A 79 -1 O ARG A 74 N GLU A 40 SHEET 4 AA2 4 GLY A 88 MSE A 94 -1 O VAL A 92 N TYR A 71 LINK OD1 ASN A 1 CA CA A 101 1555 1555 2.45 LINK O ASP A 2 CA CA A 101 1555 1555 2.32 LINK OD1 ASP A 29 CA CA A 101 1555 1555 2.63 LINK OD2 ASP A 29 CA CA A 101 1555 1555 2.43 LINK OD1 ASN A 31 CA CA A 101 1555 1555 2.46 LINK OD2 ASP A 33 CA CA A 101 1555 1555 2.33 LINK OD2 ASP A 79 CA CA A 101 1555 1555 2.37 LINK C THR A 93 N MSE A 94 1555 1555 1.33 LINK C MSE A 94 N PRO A 95 1555 1555 1.33 CISPEP 1 GLY A 51 PRO A 52 0 5.58 SITE 1 AC1 6 ASN A 1 ASP A 2 ASP A 29 ASN A 31 SITE 2 AC1 6 ASP A 33 ASP A 79 SITE 1 AC2 6 TYR A 38 LYS A 76 GLU A 84 HOH A 202 SITE 2 AC2 6 HOH A 237 HOH A 306 SITE 1 AC3 4 GLY A 42 GLY A 44 HOH A 319 HOH A 323 CRYST1 46.186 48.869 78.509 90.00 90.00 90.00 I 2 2 2 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 0.021652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012737 0.00000