HEADER HYDROLASE 06-AUG-08 3E2V TITLE CRYSTAL STRUCTURE OF AN UNCHARACTERIZED AMIDOHYDROLASE FROM TITLE 2 SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3'-5'-EXONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 307796; SOURCE 5 STRAIN: YJM789; SOURCE 6 GENE: SCY_0164; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET26 KEYWDS STRUCTURAL GENOMICS, HYDROLASE, EXONUCLEASE, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC EXPDTA X-RAY DIFFRACTION AUTHOR J.B.BONANNO,M.DICKEY,K.T.BAIN,S.HU,R.ROMERO,D.SMITH,S.WASSERMAN, AUTHOR 2 J.M.SAUDER,S.K.BURLEY,S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 3 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 10-FEB-21 3E2V 1 AUTHOR JRNL REMARK LINK REVDAT 5 14-NOV-18 3E2V 1 AUTHOR REVDAT 4 25-OCT-17 3E2V 1 REMARK REVDAT 3 13-JUL-11 3E2V 1 VERSN REVDAT 2 24-FEB-09 3E2V 1 VERSN REVDAT 1 26-AUG-08 3E2V 0 JRNL AUTH J.B.BONANNO,M.DICKEY,K.T.BAIN,S.HU,R.ROMERO,D.SMITH, JRNL AUTH 2 S.WASSERMAN,J.M.SAUDER,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF AN UNCHARACTERIZED AMIDOHYDROLASE FROM JRNL TITL 2 SACCHAROMYCES CEREVISIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 123161 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6190 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8395 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 455 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5793 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 704 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.112 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5998 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8119 ; 1.238 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 741 ; 5.365 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;35.156 ;24.710 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1065 ;11.940 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;13.338 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 906 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4475 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2917 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4154 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 541 ; 0.104 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.088 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 68 ; 0.178 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.089 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3755 ; 0.841 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5907 ; 1.366 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2521 ; 2.314 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2201 ; 3.361 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3E2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97958 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.19 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 123244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 114.708 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS HCL PH 9, 32% PEG 4K, 200MM REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE, PH 9.0, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.50350 REMARK 290 SMTRY3 2 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT IS PROBABLE MONOMER 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 MET A 25 REMARK 465 SER A 26 REMARK 465 LEU A 27 REMARK 465 THR A 28 REMARK 465 SER A 29 REMARK 465 THR A 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 ASP A 33 REMARK 465 SER A 34 REMARK 465 ASP A 123 REMARK 465 ALA A 124 REMARK 465 SER A 125 REMARK 465 GLN A 126 REMARK 465 GLY A 127 REMARK 465 ASP A 128 REMARK 465 LYS A 129 REMARK 465 ALA A 130 REMARK 465 SER A 131 REMARK 465 ALA A 132 REMARK 465 SER A 133 REMARK 465 ILE A 134 REMARK 465 ASP A 135 REMARK 465 ASN A 136 REMARK 465 PRO A 137 REMARK 465 SER A 138 REMARK 465 MET A 139 REMARK 465 ASP A 140 REMARK 465 GLY A 258 REMARK 465 ALA A 259 REMARK 465 GLU A 418 REMARK 465 GLY A 419 REMARK 465 HIS A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 MET B 25 REMARK 465 SER B 26 REMARK 465 LEU B 27 REMARK 465 THR B 28 REMARK 465 SER B 29 REMARK 465 THR B 30 REMARK 465 ALA B 31 REMARK 465 THR B 32 REMARK 465 ASP B 33 REMARK 465 SER B 34 REMARK 465 ASP B 123 REMARK 465 ALA B 124 REMARK 465 SER B 125 REMARK 465 GLN B 126 REMARK 465 GLY B 127 REMARK 465 ASP B 128 REMARK 465 LYS B 129 REMARK 465 ALA B 130 REMARK 465 SER B 131 REMARK 465 ALA B 132 REMARK 465 SER B 133 REMARK 465 ILE B 134 REMARK 465 ASP B 135 REMARK 465 ASN B 136 REMARK 465 PRO B 137 REMARK 465 SER B 138 REMARK 465 MET B 139 REMARK 465 ASP B 140 REMARK 465 GLY B 258 REMARK 465 ALA B 259 REMARK 465 GLY B 417 REMARK 465 GLU B 418 REMARK 465 GLY B 419 REMARK 465 HIS B 420 REMARK 465 HIS B 421 REMARK 465 HIS B 422 REMARK 465 HIS B 423 REMARK 465 HIS B 424 REMARK 465 HIS B 425 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 GLU A 248 CG CD OE1 OE2 REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 SER A 262 OG REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 VAL A 349 CG1 CG2 REMARK 470 ARG A 350 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 351 CG OD1 OD2 REMARK 470 GLU A 353 CG CD OE1 OE2 REMARK 470 LYS B 150 CG CD CE NZ REMARK 470 LYS B 256 CG CD CE NZ REMARK 470 SER B 262 OG REMARK 470 GLU B 348 CG CD OE1 OE2 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 ARG A 74 30.45 -99.89 REMARK 500 ALA B 230 28.35 -140.40 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 MG A 427 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 277 NE2 REMARK 620 2 ASP A 327 OD1 95.2 REMARK 620 3 HOH A 541 O 86.0 91.4 REMARK 620 4 HOH A 623 O 100.6 96.7 169.0 REMARK 620 5 HOH A 631 O 171.5 86.9 85.7 87.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 426 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 277 NE2 REMARK 620 2 ASP B 327 OD1 95.0 REMARK 620 3 HOH B 599 O 100.8 98.4 REMARK 620 4 HOH B 603 O 172.6 85.0 86.5 REMARK 620 5 HOH B 777 O 85.9 91.8 167.2 86.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 428 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 530 O REMARK 620 2 HOH B 604 O 85.1 REMARK 620 3 HOH B 771 O 85.4 169.6 REMARK 620 4 HOH B 772 O 169.7 95.5 94.7 REMARK 620 5 HOH B 773 O 83.8 88.1 95.2 85.9 REMARK 620 6 HOH B 774 O 101.6 91.7 85.9 88.7 174.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 426 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 426 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 428 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-9626A RELATED DB: TARGETDB DBREF 3E2V A 28 418 UNP A6ZKP4 A6ZKP4_YEAS7 28 418 DBREF 3E2V B 28 418 UNP A6ZKP4 A6ZKP4_YEAS7 28 418 SEQADV 3E2V MET A 25 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V SER A 26 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V LEU A 27 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V GLY A 419 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 420 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 421 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 422 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 423 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 424 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS A 425 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V MET B 25 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V SER B 26 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V LEU B 27 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V GLY B 419 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 420 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 421 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 422 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 423 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 424 UNP A6ZKP4 EXPRESSION TAG SEQADV 3E2V HIS B 425 UNP A6ZKP4 EXPRESSION TAG SEQRES 1 A 401 MET SER LEU THR SER THR ALA THR ASP SER PRO LEU LYS SEQRES 2 A 401 TYR TYR ASP ILE GLY LEU ASN LEU THR ASP PRO MET PHE SEQRES 3 A 401 HIS GLY ILE TYR ASN GLY LYS GLN TYR HIS PRO ALA ASP SEQRES 4 A 401 TYR VAL LYS LEU LEU GLU ARG ALA ALA GLN ARG HIS VAL SEQRES 5 A 401 LYS ASN ALA LEU VAL THR GLY SER SER ILE ALA GLU SER SEQRES 6 A 401 GLN SER ALA ILE GLU LEU VAL SER SER VAL LYS ASP LEU SEQRES 7 A 401 SER PRO LEU LYS LEU TYR HIS THR ILE GLY VAL HIS PRO SEQRES 8 A 401 CYS CYS VAL ASN GLU PHE ALA ASP ALA SER GLN GLY ASP SEQRES 9 A 401 LYS ALA SER ALA SER ILE ASP ASN PRO SER MET ASP GLU SEQRES 10 A 401 ALA TYR ASN GLU SER LEU TYR ALA LYS VAL ILE SER ASN SEQRES 11 A 401 PRO SER PHE ALA GLN GLY LYS LEU LYS GLU LEU TYR ASP SEQRES 12 A 401 LEU MET ASN GLN GLN ALA LYS PRO HIS ASP THR SER PHE SEQRES 13 A 401 ARG SER ILE GLY GLU ILE GLY LEU ASP TYR ASP ARG PHE SEQRES 14 A 401 HIS TYR SER SER LYS GLU MET GLN LYS VAL PHE PHE GLU SEQRES 15 A 401 GLU GLN LEU LYS ILE SER CYS LEU ASN ASP LYS LEU SER SEQRES 16 A 401 SER TYR PRO LEU PHE LEU HIS MET ARG SER ALA CYS ASP SEQRES 17 A 401 ASP PHE VAL GLN ILE LEU GLU ARG PHE VAL VAL GLY PHE SEQRES 18 A 401 THR ASP GLU LYS ASP THR PHE GLN LEU GLN LYS LEU GLY SEQRES 19 A 401 ALA SER SER SER SER GLY PHE TYR LYS PHE HIS PRO ASP SEQRES 20 A 401 ARG LYS LEU VAL VAL HIS SER PHE THR GLY SER ALA ILE SEQRES 21 A 401 ASP LEU GLN LYS LEU LEU ASN LEU SER PRO ASN ILE PHE SEQRES 22 A 401 ILE GLY VAL ASN GLY CYS SER LEU ARG THR GLU GLU ASN SEQRES 23 A 401 LEU ALA VAL VAL LYS GLN ILE PRO THR GLU ARG LEU LEU SEQRES 24 A 401 LEU GLU THR ASP ALA PRO TRP CYS GLU ILE LYS ARG THR SEQRES 25 A 401 HIS ALA SER PHE GLN TYR LEU ALA LYS TYR GLN GLU VAL SEQRES 26 A 401 ARG ASP PHE GLU TYR PRO ALA PHE LYS SER VAL LYS LYS SEQRES 27 A 401 ASN LYS LEU ALA ASP LYS LEU ASN ALA GLU GLU LEU TYR SEQRES 28 A 401 MET VAL LYS GLY ARG ASN GLU PRO CYS ASN MET GLU GLN SEQRES 29 A 401 VAL ALA ILE VAL VAL SER GLU VAL LYS ASP VAL ASP LEU SEQRES 30 A 401 ALA THR LEU ILE ASP THR THR TRP LYS THR THR CYS LYS SEQRES 31 A 401 ILE PHE GLY GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 401 MET SER LEU THR SER THR ALA THR ASP SER PRO LEU LYS SEQRES 2 B 401 TYR TYR ASP ILE GLY LEU ASN LEU THR ASP PRO MET PHE SEQRES 3 B 401 HIS GLY ILE TYR ASN GLY LYS GLN TYR HIS PRO ALA ASP SEQRES 4 B 401 TYR VAL LYS LEU LEU GLU ARG ALA ALA GLN ARG HIS VAL SEQRES 5 B 401 LYS ASN ALA LEU VAL THR GLY SER SER ILE ALA GLU SER SEQRES 6 B 401 GLN SER ALA ILE GLU LEU VAL SER SER VAL LYS ASP LEU SEQRES 7 B 401 SER PRO LEU LYS LEU TYR HIS THR ILE GLY VAL HIS PRO SEQRES 8 B 401 CYS CYS VAL ASN GLU PHE ALA ASP ALA SER GLN GLY ASP SEQRES 9 B 401 LYS ALA SER ALA SER ILE ASP ASN PRO SER MET ASP GLU SEQRES 10 B 401 ALA TYR ASN GLU SER LEU TYR ALA LYS VAL ILE SER ASN SEQRES 11 B 401 PRO SER PHE ALA GLN GLY LYS LEU LYS GLU LEU TYR ASP SEQRES 12 B 401 LEU MET ASN GLN GLN ALA LYS PRO HIS ASP THR SER PHE SEQRES 13 B 401 ARG SER ILE GLY GLU ILE GLY LEU ASP TYR ASP ARG PHE SEQRES 14 B 401 HIS TYR SER SER LYS GLU MET GLN LYS VAL PHE PHE GLU SEQRES 15 B 401 GLU GLN LEU LYS ILE SER CYS LEU ASN ASP LYS LEU SER SEQRES 16 B 401 SER TYR PRO LEU PHE LEU HIS MET ARG SER ALA CYS ASP SEQRES 17 B 401 ASP PHE VAL GLN ILE LEU GLU ARG PHE VAL VAL GLY PHE SEQRES 18 B 401 THR ASP GLU LYS ASP THR PHE GLN LEU GLN LYS LEU GLY SEQRES 19 B 401 ALA SER SER SER SER GLY PHE TYR LYS PHE HIS PRO ASP SEQRES 20 B 401 ARG LYS LEU VAL VAL HIS SER PHE THR GLY SER ALA ILE SEQRES 21 B 401 ASP LEU GLN LYS LEU LEU ASN LEU SER PRO ASN ILE PHE SEQRES 22 B 401 ILE GLY VAL ASN GLY CYS SER LEU ARG THR GLU GLU ASN SEQRES 23 B 401 LEU ALA VAL VAL LYS GLN ILE PRO THR GLU ARG LEU LEU SEQRES 24 B 401 LEU GLU THR ASP ALA PRO TRP CYS GLU ILE LYS ARG THR SEQRES 25 B 401 HIS ALA SER PHE GLN TYR LEU ALA LYS TYR GLN GLU VAL SEQRES 26 B 401 ARG ASP PHE GLU TYR PRO ALA PHE LYS SER VAL LYS LYS SEQRES 27 B 401 ASN LYS LEU ALA ASP LYS LEU ASN ALA GLU GLU LEU TYR SEQRES 28 B 401 MET VAL LYS GLY ARG ASN GLU PRO CYS ASN MET GLU GLN SEQRES 29 B 401 VAL ALA ILE VAL VAL SER GLU VAL LYS ASP VAL ASP LEU SEQRES 30 B 401 ALA THR LEU ILE ASP THR THR TRP LYS THR THR CYS LYS SEQRES 31 B 401 ILE PHE GLY GLU GLY HIS HIS HIS HIS HIS HIS HET GOL A 1 6 HET GOL A 426 6 HET MG A 427 1 HET GOL B 1 6 HET MG B 426 1 HET GOL B 427 6 HET MG B 428 1 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 4(C3 H8 O3) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *704(H2 O) HELIX 1 1 ASP A 47 HIS A 51 5 5 HELIX 2 2 ASP A 63 ARG A 74 1 12 HELIX 3 3 SER A 85 LYS A 100 1 16 HELIX 4 4 HIS A 114 ALA A 122 5 9 HELIX 5 5 GLU A 141 ASN A 154 1 14 HELIX 6 6 PRO A 155 LYS A 174 1 20 HELIX 7 7 SER A 197 SER A 212 1 16 HELIX 8 8 ASN A 215 SER A 220 1 6 HELIX 9 9 ALA A 230 GLY A 244 1 15 HELIX 10 10 GLN A 253 LEU A 257 5 5 HELIX 11 11 SER A 282 SER A 293 1 12 HELIX 12 12 ASN A 301 ARG A 306 5 6 HELIX 13 13 THR A 307 GLN A 316 1 10 HELIX 14 14 ILE A 317 GLU A 320 5 4 HELIX 15 15 SER A 339 ARG A 350 1 12 HELIX 16 16 LYS A 361 LEU A 369 5 9 HELIX 17 17 GLU A 382 CYS A 384 5 3 HELIX 18 18 ASN A 385 ASP A 398 1 14 HELIX 19 19 ASP A 400 GLY A 417 1 18 HELIX 20 20 ASP B 47 HIS B 51 5 5 HELIX 21 21 ASP B 63 ARG B 74 1 12 HELIX 22 22 SER B 85 LYS B 100 1 16 HELIX 23 23 HIS B 114 ALA B 122 5 9 HELIX 24 24 GLU B 141 ASN B 154 1 14 HELIX 25 25 PRO B 155 LYS B 174 1 20 HELIX 26 26 SER B 197 SER B 212 1 16 HELIX 27 27 ASN B 215 SER B 220 1 6 HELIX 28 28 ALA B 230 GLY B 244 1 15 HELIX 29 29 GLN B 253 LEU B 257 5 5 HELIX 30 30 SER B 282 SER B 293 1 12 HELIX 31 31 ASN B 301 ARG B 306 5 6 HELIX 32 32 THR B 307 GLN B 316 1 10 HELIX 33 33 ILE B 317 GLU B 320 5 4 HELIX 34 34 SER B 339 ARG B 350 1 12 HELIX 35 35 LYS B 361 LEU B 369 5 9 HELIX 36 36 GLU B 382 CYS B 384 5 3 HELIX 37 37 ASN B 385 ASP B 398 1 14 HELIX 38 38 ASP B 400 PHE B 416 1 17 SHEET 1 A 8 TYR A 38 LEU A 43 0 SHEET 2 A 8 VAL A 76 VAL A 81 1 O LEU A 80 N ASP A 40 SHEET 3 A 8 LYS A 106 ILE A 111 1 O TYR A 108 N VAL A 81 SHEET 4 A 8 PHE A 180 ASP A 189 1 O ARG A 181 N HIS A 109 SHEET 5 A 8 LEU A 223 ARG A 228 1 O PHE A 224 N ILE A 183 SHEET 6 A 8 LEU A 274 VAL A 276 1 O VAL A 275 N LEU A 225 SHEET 7 A 8 ILE A 296 VAL A 300 1 O GLY A 299 N VAL A 276 SHEET 8 A 8 LEU A 322 LEU A 324 1 O LEU A 323 N VAL A 300 SHEET 1 B 2 ILE A 53 TYR A 54 0 SHEET 2 B 2 LYS A 57 GLN A 58 -1 O LYS A 57 N TYR A 54 SHEET 1 C 2 PHE A 245 THR A 246 0 SHEET 2 C 2 PHE A 265 TYR A 266 -1 O TYR A 266 N PHE A 245 SHEET 1 D 2 LYS A 358 VAL A 360 0 SHEET 2 D 2 TYR A 375 VAL A 377 1 O MET A 376 N LYS A 358 SHEET 1 E 8 TYR B 38 LEU B 43 0 SHEET 2 E 8 VAL B 76 VAL B 81 1 O LEU B 80 N ASP B 40 SHEET 3 E 8 LYS B 106 ILE B 111 1 O TYR B 108 N VAL B 81 SHEET 4 E 8 PHE B 180 ASP B 189 1 O ARG B 181 N HIS B 109 SHEET 5 E 8 LEU B 223 ARG B 228 1 O PHE B 224 N ILE B 183 SHEET 6 E 8 LEU B 274 HIS B 277 1 O VAL B 275 N LEU B 225 SHEET 7 E 8 ILE B 296 VAL B 300 1 O GLY B 299 N VAL B 276 SHEET 8 E 8 LEU B 322 LEU B 324 1 O LEU B 323 N VAL B 300 SHEET 1 F 2 ILE B 53 TYR B 54 0 SHEET 2 F 2 LYS B 57 GLN B 58 -1 O LYS B 57 N TYR B 54 SHEET 1 G 2 PHE B 245 THR B 246 0 SHEET 2 G 2 PHE B 265 TYR B 266 -1 O TYR B 266 N PHE B 245 SHEET 1 H 2 LYS B 358 VAL B 360 0 SHEET 2 H 2 TYR B 375 VAL B 377 1 O MET B 376 N LYS B 358 SSBOND 1 CYS A 116 CYS A 117 1555 1555 2.09 SSBOND 2 CYS A 303 CYS A 331 1555 1555 2.07 SSBOND 3 CYS B 116 CYS B 117 1555 1555 2.09 SSBOND 4 CYS B 303 CYS B 331 1555 1555 2.06 LINK NE2 HIS A 277 MG MG A 427 1555 1555 2.21 LINK OD1 ASP A 327 MG MG A 427 1555 1555 2.25 LINK MG MG A 427 O HOH A 541 1555 1555 2.06 LINK MG MG A 427 O HOH A 623 1555 1555 2.01 LINK MG MG A 427 O HOH A 631 1555 1555 2.06 LINK NE2 HIS B 277 MG MG B 426 1555 1555 2.19 LINK OD1 ASP B 327 MG MG B 426 1555 1555 2.21 LINK MG MG B 426 O HOH B 599 1555 1555 1.88 LINK MG MG B 426 O HOH B 603 1555 1555 2.13 LINK MG MG B 426 O HOH B 777 1555 1555 1.94 LINK MG MG B 428 O HOH B 530 1555 1555 2.25 LINK MG MG B 428 O HOH B 604 1555 1555 2.09 LINK MG MG B 428 O HOH B 771 1555 1555 2.11 LINK MG MG B 428 O HOH B 772 1555 1555 2.06 LINK MG MG B 428 O HOH B 773 1555 1555 2.03 LINK MG MG B 428 O HOH B 774 1555 1555 2.06 CISPEP 1 GLY A 184 GLU A 185 0 -2.14 CISPEP 2 GLY A 184 GLU A 185 0 -1.01 CISPEP 3 ALA A 328 PRO A 329 0 10.58 CISPEP 4 TYR A 354 PRO A 355 0 -8.61 CISPEP 5 GLY B 184 GLU B 185 0 -1.38 CISPEP 6 GLY B 184 GLU B 185 0 -0.61 CISPEP 7 ALA B 328 PRO B 329 0 11.20 CISPEP 8 TYR B 354 PRO B 355 0 -4.26 SITE 1 AC1 8 CYS A 213 SER A 260 SER A 261 GLY A 264 SITE 2 AC1 8 PHE A 265 TYR A 266 HOH A 488 HOH A 627 SITE 1 AC2 9 GLU A 332 SER A 359 MET A 376 VAL A 377 SITE 2 AC2 9 GLY A 379 ARG A 380 ASN A 385 HOH A 509 SITE 3 AC2 9 HOH A 539 SITE 1 AC3 6 HIS A 277 ASP A 327 HOH A 454 HOH A 541 SITE 2 AC3 6 HOH A 623 HOH A 631 SITE 1 AC4 8 CYS B 213 SER B 260 SER B 261 GLY B 264 SITE 2 AC4 8 PHE B 265 TYR B 266 HOH B 487 HOH B 718 SITE 1 AC5 7 HIS B 277 SER B 278 ASP B 327 HOH B 435 SITE 2 AC5 7 HOH B 599 HOH B 603 HOH B 777 SITE 1 AC6 9 GLU B 332 SER B 359 MET B 376 VAL B 377 SITE 2 AC6 9 GLY B 379 ARG B 380 ASN B 385 HOH B 510 SITE 3 AC6 9 HOH B 611 SITE 1 AC7 6 HOH B 530 HOH B 604 HOH B 771 HOH B 772 SITE 2 AC7 6 HOH B 773 HOH B 774 CRYST1 62.532 55.007 115.260 90.00 95.85 90.00 P 1 21 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 0.015992 0.000000 0.001638 0.00000 SCALE2 0.000000 0.018179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008721 0.00000