HEADER HYDROLASE 21-AUG-18 6HF6 TITLE CRYSTAL STRUCTURE OF THE PROTEASE 1 (E29A,E60A,E80A) FROM PYROCOCCUS TITLE 2 HORIKOSHII CO-CRYSTALLIZED WITH TB-XO4. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEGLYCASE PH1704; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: INTRACELLULAR PROTEASE PH1704; COMPND 5 EC: 3.5.1.124,3.4.22.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII (STRAIN ATCC 700860 / DSM SOURCE 3 12428 / JCM 9974 / NBRC 100139 / OT-3); SOURCE 4 ORGANISM_TAXID: 70601; SOURCE 5 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 6 GENE: PH1704; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MESHANDCOLLECT, DE NOVO PHASING, SAD, CRYSTALLIZATION, TB-XO4, KEYWDS 2 CRYSTALLOPHORE, LANTHANIDE COMPLEX, MULTI-CRYSTALS DATA COLLECTION, KEYWDS 3 CCCLUSTER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.ENGILBERGE,T.WAGNER,G.SANTONI,C.BREYTON,S.SHIMA,B.FRANZETTI, AUTHOR 2 F.RIOBE,O.MAURY,E.GIRARD REVDAT 2 21-AUG-19 6HF6 1 JRNL REVDAT 1 19-JUN-19 6HF6 0 JRNL AUTH S.ENGILBERGE,T.WAGNER,G.SANTONI,C.BREYTON,S.SHIMA, JRNL AUTH 2 B.FRANZETTI,F.RIOBE,O.MAURY,E.GIRARD JRNL TITL PROTEIN CRYSTAL STRUCTURE DETERMINATION WITH THE JRNL TITL 2 CRYSTALLOPHORE, A NUCLEATING AND PHASING AGENT. JRNL REF J.APPL.CRYSTALLOGR. V. 52 722 2019 JRNL REFN ISSN 0021-8898 JRNL PMID 31396026 JRNL DOI 10.1107/S1600576719006381 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 69185 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 3384 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 5065 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2034 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4816 REMARK 3 BIN R VALUE (WORKING SET) : 0.2033 REMARK 3 BIN FREE R VALUE : 0.2051 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.92 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 249 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3906 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 115 REMARK 3 SOLVENT ATOMS : 552 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.55270 REMARK 3 B22 (A**2) : 8.55270 REMARK 3 B33 (A**2) : -17.10530 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.230 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.105 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.098 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.118 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.093 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 8146 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 14760 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1770 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1258 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 8146 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 503 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 9149 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.86 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.79 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 33.7974 26.4045 -14.4880 REMARK 3 T TENSOR REMARK 3 T11: -0.1402 T22: -0.0430 REMARK 3 T33: -0.0018 T12: -0.0184 REMARK 3 T13: -0.0160 T23: -0.0549 REMARK 3 L TENSOR REMARK 3 L11: 1.7212 L22: 0.9292 REMARK 3 L33: 0.5284 L12: -0.0380 REMARK 3 L13: -0.4147 L23: 0.1033 REMARK 3 S TENSOR REMARK 3 S11: -0.0185 S12: 0.2919 S13: -0.0855 REMARK 3 S21: -0.0643 S22: 0.0286 S23: -0.0179 REMARK 3 S31: 0.0183 S32: -0.0044 S33: -0.0102 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 63.3816 29.7272 -14.9103 REMARK 3 T TENSOR REMARK 3 T11: -0.1629 T22: -0.0647 REMARK 3 T33: 0.0224 T12: -0.0009 REMARK 3 T13: 0.0173 T23: -0.0493 REMARK 3 L TENSOR REMARK 3 L11: 2.1906 L22: 1.0661 REMARK 3 L33: 0.9098 L12: 0.4554 REMARK 3 L13: -0.1673 L23: 0.0557 REMARK 3 S TENSOR REMARK 3 S11: -0.0616 S12: 0.1283 S13: -0.1511 REMARK 3 S21: -0.0065 S22: 0.0171 S23: -0.0552 REMARK 3 S31: 0.0282 S32: -0.0075 S33: 0.0445 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 67.7105 60.3439 -13.8824 REMARK 3 T TENSOR REMARK 3 T11: -0.1732 T22: -0.1568 REMARK 3 T33: 0.2235 T12: 0.0061 REMARK 3 T13: 0.0883 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.2274 L22: 1.5982 REMARK 3 L33: 1.3973 L12: -0.3034 REMARK 3 L13: -0.4365 L23: 0.8474 REMARK 3 S TENSOR REMARK 3 S11: 0.1337 S12: 0.0660 S13: 0.4467 REMARK 3 S21: -0.1744 S22: 0.0840 S23: 0.0034 REMARK 3 S31: -0.2463 S32: 0.0124 S33: -0.2177 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): 48.6912 44.9728 -9.8334 REMARK 3 T TENSOR REMARK 3 T11: -0.0964 T22: -0.0580 REMARK 3 T33: 0.0359 T12: 0.0265 REMARK 3 T13: -0.0700 T23: -0.1493 REMARK 3 L TENSOR REMARK 3 L11: 2.3279 L22: 0.3483 REMARK 3 L33: 0.1307 L12: -0.9844 REMARK 3 L13: 0.1940 L23: -0.1766 REMARK 3 S TENSOR REMARK 3 S11: -0.0044 S12: 0.0597 S13: 0.1659 REMARK 3 S21: 0.1081 S22: 0.0461 S23: 0.1347 REMARK 3 S31: -0.1980 S32: 0.2399 S33: -0.0417 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200009197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.648 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69275 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 18.20 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION : 10 MG.ML-1 REMARK 280 CRYSTALLIZATION DROP : 1.5 UL OF PROTEIN AND 1.5 UL OF THE REMARK 280 PRECIPITANT. CRYSTALLIZATION SOLUTION : 2.8 TO 3.4 SODIUM REMARK 280 MALONATE PH 5.5. NOTE : TB-XO4 WAS SOLUBILIZED WITH THE PROTEIN REMARK 280 SOLUTION FOR A FINAL CONCENTRATION OF 10 MM, 1 HOUR BEFORE TO REMARK 280 PERFORM THE CRYSTALLIZATION DROP., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 65.15500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.31000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.57750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.31000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.31000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 97.73250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.31000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.31000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.57750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.31000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.31000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 97.73250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.15500 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: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HD3 ARG A 71 HD3 ARG A 71 7555 1.17 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 CYS A 100 -117.00 59.01 REMARK 500 CYS B 100 -116.71 59.40 REMARK 500 CYS C 100 -116.29 58.83 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 TB A 204 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 10 OE1 REMARK 620 2 HOH A 424 O 86.6 REMARK 620 3 HOH A 456 O 161.7 88.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 7MT A 201 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MLI A 202 O8 REMARK 620 2 7MT A 201 N23 70.5 REMARK 620 3 7MT A 201 N02 151.7 85.2 REMARK 620 4 7MT A 201 N06 139.5 124.0 66.5 REMARK 620 5 7MT A 201 N09 111.7 60.7 65.1 63.6 REMARK 620 6 7MT A 201 O26 68.8 65.7 88.5 150.5 121.1 REMARK 620 7 7MT A 201 N17 118.6 123.3 63.3 86.5 127.3 67.6 REMARK 620 8 7MT A 201 O27 82.6 152.0 118.3 81.8 140.9 97.9 63.3 REMARK 620 9 MLI A 202 O9 51.4 87.2 144.0 89.4 80.5 119.9 145.0 81.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 7MT B 201 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MLI B 202 O8 REMARK 620 2 7MT B 201 N23 73.3 REMARK 620 3 7MT B 201 N02 154.0 85.8 REMARK 620 4 7MT B 201 N06 141.6 128.4 64.2 REMARK 620 5 7MT B 201 N09 117.1 64.0 64.1 65.2 REMARK 620 6 7MT B 201 O26 67.9 62.5 88.9 147.3 121.0 REMARK 620 7 7MT B 201 N17 112.7 120.9 65.0 84.6 128.2 66.5 REMARK 620 8 7MT B 201 O27 76.9 148.4 119.1 82.3 142.3 96.6 62.4 REMARK 620 9 MLI B 202 O9 47.6 86.1 147.9 97.8 84.5 114.4 143.3 81.6 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB B 203 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 397 O REMARK 620 2 HOH B 450 O 72.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 7MT C 201 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MLI C 202 O6 REMARK 620 2 7MT C 201 N23 87.0 REMARK 620 3 7MT C 201 N02 148.7 84.7 REMARK 620 4 7MT C 201 N06 103.3 123.4 58.1 REMARK 620 5 7MT C 201 N09 88.2 63.6 61.1 61.4 REMARK 620 6 7MT C 201 O26 120.0 66.2 83.7 136.6 119.9 REMARK 620 7 7MT C 201 N17 145.1 122.5 60.7 77.1 120.1 65.7 REMARK 620 8 7MT C 201 O27 82.7 155.9 114.9 80.4 137.3 100.5 62.8 REMARK 620 9 MLI C 202 O7 46.7 81.5 158.6 143.2 124.9 75.8 114.4 75.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB C 203 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 417 O REMARK 620 2 HOH C 373 O 94.1 REMARK 620 3 HOH C 364 O 76.2 71.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TB A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TB B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MT C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TB C 203 DBREF 6HF6 A 1 166 UNP O59413 DEGLY_PYRHO 1 166 DBREF 6HF6 B 1 166 UNP O59413 DEGLY_PYRHO 1 166 DBREF 6HF6 C 1 166 UNP O59413 DEGLY_PYRHO 1 166 SEQADV 6HF6 ALA A 29 UNP O59413 GLU 29 ENGINEERED MUTATION SEQADV 6HF6 ALA A 60 UNP O59413 GLU 60 ENGINEERED MUTATION SEQADV 6HF6 ALA A 80 UNP O59413 GLU 80 ENGINEERED MUTATION SEQADV 6HF6 ALA B 29 UNP O59413 GLU 29 ENGINEERED MUTATION SEQADV 6HF6 ALA B 60 UNP O59413 GLU 60 ENGINEERED MUTATION SEQADV 6HF6 ALA B 80 UNP O59413 GLU 80 ENGINEERED MUTATION SEQADV 6HF6 ALA C 29 UNP O59413 GLU 29 ENGINEERED MUTATION SEQADV 6HF6 ALA C 60 UNP O59413 GLU 60 ENGINEERED MUTATION SEQADV 6HF6 ALA C 80 UNP O59413 GLU 80 ENGINEERED MUTATION SEQRES 1 A 166 MET LYS VAL LEU PHE LEU THR ALA ASN GLU PHE GLU ASP SEQRES 2 A 166 VAL GLU LEU ILE TYR PRO TYR HIS ARG LEU LYS GLU GLU SEQRES 3 A 166 GLY HIS ALA VAL TYR ILE ALA SER PHE GLU ARG GLY THR SEQRES 4 A 166 ILE THR GLY LYS HIS GLY TYR SER VAL LYS VAL ASP LEU SEQRES 5 A 166 THR PHE ASP LYS VAL ASN PRO ALA GLU PHE ASP ALA LEU SEQRES 6 A 166 VAL LEU PRO GLY GLY ARG ALA PRO GLU ARG VAL ARG LEU SEQRES 7 A 166 ASN ALA LYS ALA VAL SER ILE ALA ARG LYS MET PHE SER SEQRES 8 A 166 GLU GLY LYS PRO VAL ALA SER ILE CYS HIS GLY PRO GLN SEQRES 9 A 166 ILE LEU ILE SER ALA GLY VAL LEU ARG GLY ARG LYS GLY SEQRES 10 A 166 THR SER TYR PRO GLY ILE LYS ASP ASP MET ILE ASN ALA SEQRES 11 A 166 GLY VAL GLU TRP VAL ASP ALA GLU VAL VAL VAL ASP GLY SEQRES 12 A 166 ASN TRP VAL SER SER ARG VAL PRO ALA ASP LEU TYR ALA SEQRES 13 A 166 TRP MET ARG GLU PHE VAL LYS LEU LEU LYS SEQRES 1 B 166 MET LYS VAL LEU PHE LEU THR ALA ASN GLU PHE GLU ASP SEQRES 2 B 166 VAL GLU LEU ILE TYR PRO TYR HIS ARG LEU LYS GLU GLU SEQRES 3 B 166 GLY HIS ALA VAL TYR ILE ALA SER PHE GLU ARG GLY THR SEQRES 4 B 166 ILE THR GLY LYS HIS GLY TYR SER VAL LYS VAL ASP LEU SEQRES 5 B 166 THR PHE ASP LYS VAL ASN PRO ALA GLU PHE ASP ALA LEU SEQRES 6 B 166 VAL LEU PRO GLY GLY ARG ALA PRO GLU ARG VAL ARG LEU SEQRES 7 B 166 ASN ALA LYS ALA VAL SER ILE ALA ARG LYS MET PHE SER SEQRES 8 B 166 GLU GLY LYS PRO VAL ALA SER ILE CYS HIS GLY PRO GLN SEQRES 9 B 166 ILE LEU ILE SER ALA GLY VAL LEU ARG GLY ARG LYS GLY SEQRES 10 B 166 THR SER TYR PRO GLY ILE LYS ASP ASP MET ILE ASN ALA SEQRES 11 B 166 GLY VAL GLU TRP VAL ASP ALA GLU VAL VAL VAL ASP GLY SEQRES 12 B 166 ASN TRP VAL SER SER ARG VAL PRO ALA ASP LEU TYR ALA SEQRES 13 B 166 TRP MET ARG GLU PHE VAL LYS LEU LEU LYS SEQRES 1 C 166 MET LYS VAL LEU PHE LEU THR ALA ASN GLU PHE GLU ASP SEQRES 2 C 166 VAL GLU LEU ILE TYR PRO TYR HIS ARG LEU LYS GLU GLU SEQRES 3 C 166 GLY HIS ALA VAL TYR ILE ALA SER PHE GLU ARG GLY THR SEQRES 4 C 166 ILE THR GLY LYS HIS GLY TYR SER VAL LYS VAL ASP LEU SEQRES 5 C 166 THR PHE ASP LYS VAL ASN PRO ALA GLU PHE ASP ALA LEU SEQRES 6 C 166 VAL LEU PRO GLY GLY ARG ALA PRO GLU ARG VAL ARG LEU SEQRES 7 C 166 ASN ALA LYS ALA VAL SER ILE ALA ARG LYS MET PHE SER SEQRES 8 C 166 GLU GLY LYS PRO VAL ALA SER ILE CYS HIS GLY PRO GLN SEQRES 9 C 166 ILE LEU ILE SER ALA GLY VAL LEU ARG GLY ARG LYS GLY SEQRES 10 C 166 THR SER TYR PRO GLY ILE LYS ASP ASP MET ILE ASN ALA SEQRES 11 C 166 GLY VAL GLU TRP VAL ASP ALA GLU VAL VAL VAL ASP GLY SEQRES 12 C 166 ASN TRP VAL SER SER ARG VAL PRO ALA ASP LEU TYR ALA SEQRES 13 C 166 TRP MET ARG GLU PHE VAL LYS LEU LEU LYS HET 7MT A 201 53 HET MLI A 202 9 HET TB A 203 1 HET TB A 204 1 HET 7MT B 201 53 HET MLI B 202 9 HET TB B 203 1 HET 7MT C 201 53 HET MLI C 202 9 HET TB C 203 1 HETNAM 7MT TB-XO4 HETNAM MLI MALONATE ION HETNAM TB TERBIUM(III) ION FORMUL 4 7MT 3(C20 H23 N5 O4 TB 5+) FORMUL 5 MLI 3(C3 H2 O4 2-) FORMUL 6 TB 4(TB 3+) FORMUL 14 HOH *552(H2 O) HELIX 1 AA1 GLU A 12 GLU A 26 1 15 HELIX 2 AA2 ASP A 55 VAL A 57 5 3 HELIX 3 AA3 ASN A 58 PHE A 62 5 5 HELIX 4 AA4 ARG A 71 ARG A 77 1 7 HELIX 5 AA5 ASN A 79 GLU A 92 1 14 HELIX 6 AA6 PRO A 103 GLY A 110 1 8 HELIX 7 AA7 TYR A 120 GLY A 122 5 3 HELIX 8 AA8 ILE A 123 ALA A 130 1 8 HELIX 9 AA9 VAL A 150 ALA A 152 5 3 HELIX 10 AB1 ASP A 153 LYS A 166 1 14 HELIX 11 AB2 GLU B 12 GLU B 26 1 15 HELIX 12 AB3 ASP B 55 VAL B 57 5 3 HELIX 13 AB4 ASN B 58 PHE B 62 5 5 HELIX 14 AB5 ARG B 71 ARG B 77 1 7 HELIX 15 AB6 ASN B 79 GLU B 92 1 14 HELIX 16 AB7 PRO B 103 GLY B 110 1 8 HELIX 17 AB8 TYR B 120 GLY B 122 5 3 HELIX 18 AB9 ILE B 123 ALA B 130 1 8 HELIX 19 AC1 VAL B 150 ALA B 152 5 3 HELIX 20 AC2 ASP B 153 LYS B 166 1 14 HELIX 21 AC3 GLU C 12 GLU C 26 1 15 HELIX 22 AC4 ASP C 55 VAL C 57 5 3 HELIX 23 AC5 ASN C 58 PHE C 62 5 5 HELIX 24 AC6 ARG C 71 ARG C 77 1 7 HELIX 25 AC7 ASN C 79 GLU C 92 1 14 HELIX 26 AC8 PRO C 103 GLY C 110 1 8 HELIX 27 AC9 TYR C 120 GLY C 122 5 3 HELIX 28 AD1 ILE C 123 ALA C 130 1 8 HELIX 29 AD2 VAL C 150 ALA C 152 5 3 HELIX 30 AD3 ASP C 153 LYS C 166 1 14 SHEET 1 AA1 7 LEU A 52 THR A 53 0 SHEET 2 AA1 7 ALA A 29 SER A 34 1 N SER A 34 O LEU A 52 SHEET 3 AA1 7 LYS A 2 LEU A 6 1 N VAL A 3 O ALA A 29 SHEET 4 AA1 7 ALA A 64 LEU A 67 1 O ALA A 64 N LEU A 4 SHEET 5 AA1 7 VAL A 96 ILE A 99 1 O ALA A 97 N LEU A 67 SHEET 6 AA1 7 TRP A 145 SER A 148 1 O VAL A 146 N VAL A 96 SHEET 7 AA1 7 VAL A 140 ASP A 142 -1 N ASP A 142 O TRP A 145 SHEET 1 AA2 2 GLY A 38 THR A 41 0 SHEET 2 AA2 2 SER A 47 VAL A 50 -1 O VAL A 50 N GLY A 38 SHEET 1 AA3 2 LYS A 116 GLY A 117 0 SHEET 2 AA3 2 GLU A 133 TRP A 134 1 O GLU A 133 N GLY A 117 SHEET 1 AA4 7 LEU B 52 THR B 53 0 SHEET 2 AA4 7 ALA B 29 SER B 34 1 N SER B 34 O LEU B 52 SHEET 3 AA4 7 LYS B 2 LEU B 6 1 N VAL B 3 O ALA B 29 SHEET 4 AA4 7 ALA B 64 LEU B 67 1 O ALA B 64 N LEU B 4 SHEET 5 AA4 7 VAL B 96 ILE B 99 1 O ALA B 97 N LEU B 67 SHEET 6 AA4 7 TRP B 145 SER B 148 1 O VAL B 146 N VAL B 96 SHEET 7 AA4 7 VAL B 140 ASP B 142 -1 N ASP B 142 O TRP B 145 SHEET 1 AA5 2 GLY B 38 THR B 41 0 SHEET 2 AA5 2 SER B 47 VAL B 50 -1 O VAL B 50 N GLY B 38 SHEET 1 AA6 2 LYS B 116 GLY B 117 0 SHEET 2 AA6 2 GLU B 133 TRP B 134 1 O GLU B 133 N GLY B 117 SHEET 1 AA7 7 LEU C 52 THR C 53 0 SHEET 2 AA7 7 ALA C 29 SER C 34 1 N SER C 34 O LEU C 52 SHEET 3 AA7 7 LYS C 2 LEU C 6 1 N VAL C 3 O ALA C 29 SHEET 4 AA7 7 ALA C 64 LEU C 67 1 O ALA C 64 N LEU C 4 SHEET 5 AA7 7 VAL C 96 ILE C 99 1 O ALA C 97 N LEU C 67 SHEET 6 AA7 7 TRP C 145 SER C 148 1 O VAL C 146 N VAL C 96 SHEET 7 AA7 7 VAL C 140 ASP C 142 -1 N ASP C 142 O TRP C 145 SHEET 1 AA8 2 GLY C 38 THR C 41 0 SHEET 2 AA8 2 SER C 47 VAL C 50 -1 O VAL C 50 N GLY C 38 SHEET 1 AA9 2 LYS C 116 GLY C 117 0 SHEET 2 AA9 2 GLU C 133 TRP C 134 1 O GLU C 133 N GLY C 117 LINK OE1 GLU A 10 TB TB A 204 1555 1555 2.34 LINK TB 7MT A 201 O8 MLI A 202 1555 1555 2.63 LINK TB 7MT A 201 O9 MLI A 202 1555 1555 2.63 LINK TB TB A 204 O HOH A 424 1555 1555 3.25 LINK TB 7MT B 201 O8 MLI B 202 1555 1555 2.72 LINK TB 7MT B 201 O9 MLI B 202 1555 1555 2.80 LINK TB TB B 203 O HOH B 397 1555 1555 2.89 LINK TB TB B 203 O HOH B 450 1555 1555 2.87 LINK TB 7MT C 201 O6 MLI C 202 1555 1555 3.00 LINK TB 7MT C 201 O7 MLI C 202 1555 1555 2.58 LINK TB TB C 203 O HOH B 417 1555 1555 3.08 LINK TB TB C 203 O HOH C 373 1555 1555 2.84 LINK TB TB C 203 O HOH C 364 1555 1555 2.68 LINK TB TB A 203 O HOH A 433 1555 7555 3.42 LINK TB TB A 204 O HOH A 456 1555 7555 2.95 SITE 1 AC1 6 ALA A 8 ASN A 9 PHE A 35 GLU A 36 SITE 2 AC1 6 ARG A 75 MLI A 202 SITE 1 AC2 3 ASN A 9 ARG A 75 7MT A 201 SITE 1 AC3 2 GLU A 10 HOH A 456 SITE 1 AC4 7 ALA B 8 ASN B 9 PHE B 35 GLU B 36 SITE 2 AC4 7 ARG B 75 MLI B 202 HOH B 386 SITE 1 AC5 4 ASN B 9 ARG B 75 7MT B 201 HOH B 386 SITE 1 AC6 2 HOH B 397 HOH B 450 SITE 1 AC7 6 ALA C 8 ASN C 9 PHE C 35 GLU C 36 SITE 2 AC7 6 ARG C 75 MLI C 202 SITE 1 AC8 3 ASN C 9 ARG C 75 7MT C 201 SITE 1 AC9 3 HOH B 417 HOH C 364 HOH C 373 CRYST1 124.620 124.620 130.310 90.00 90.00 90.00 P 41 21 2 24 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 0.008024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007674 0.00000