HEADER HYDROLASE 02-OCT-06 2IK7 TITLE YEAST INORGANIC PYROPHOSPHATASE VARIANT D120N WITH MAGNESIUM AND TITLE 2 PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INORGANIC PYROPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE; COMPND 5 EC: 3.6.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: IPP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKW9 KEYWDS INORGANIC PYROPHOSPHATASE, STRUCTURE-FUNCTION, MUTAGENESIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.OKSANEN,A.K.AHONEN,H.TUOMINEN,V.TUOMINEN,R.LAHTI,A.GOLDMAN, AUTHOR 2 P.HEIKINHEIMO REVDAT 4 30-AUG-23 2IK7 1 REMARK REVDAT 3 20-OCT-21 2IK7 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2IK7 1 VERSN REVDAT 1 13-FEB-07 2IK7 0 JRNL AUTH E.OKSANEN,A.K.AHONEN,H.TUOMINEN,V.TUOMINEN,R.LAHTI, JRNL AUTH 2 A.GOLDMAN,P.HEIKINHEIMO JRNL TITL A COMPLETE STRUCTURAL DESCRIPTION OF THE CATALYTIC CYCLE OF JRNL TITL 2 YEAST PYROPHOSPHATASE. JRNL REF BIOCHEMISTRY V. 46 1228 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17260952 JRNL DOI 10.1021/BI0619977 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 4.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44163 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2370 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2671 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.347 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4549 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3992 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6192 ; 1.503 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9384 ; 0.864 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 555 ; 6.859 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 680 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5019 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 849 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1005 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4835 ; 0.252 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2442 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 608 ; 0.210 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.104 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.332 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.366 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.254 ; 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): 2798 ; 0.748 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4548 ; 1.287 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1751 ; 2.227 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1644 ; 3.392 ; 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 2IK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50505 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.09100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54200 REMARK 200 R SYM FOR SHELL (I) : 0.54200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1HUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% MPD, 10 MM MGCL2, 1 MM PO4-, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 277K, PH 6.00 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 46.50000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 PRO A 248 REMARK 465 ASP A 249 REMARK 465 THR A 250 REMARK 465 LEU A 266 REMARK 465 ILE A 282 REMARK 465 SER A 283 REMARK 465 GLY A 284 REMARK 465 SER A 285 REMARK 465 VAL A 286 REMARK 465 SER B 283 REMARK 465 GLY B 284 REMARK 465 SER B 285 REMARK 465 VAL B 286 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 LYS A 24 CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 GLN A 202 CD OE1 NE2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 LYS A 220 CD CE NZ REMARK 470 LYS A 233 CD CE NZ REMARK 470 LYS A 238 CD CE NZ REMARK 470 SER A 254 OG REMARK 470 LYS A 274 CD CE NZ REMARK 470 GLU B 39 CG CD OE1 OE2 REMARK 470 LYS B 73 CD CE NZ REMARK 470 LYS B 167 CD CE NZ REMARK 470 LYS B 233 CD CE NZ 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 C PHE A 281 O HOH A 411 1.81 REMARK 500 O HOH B 519 O HOH B 641 1.84 REMARK 500 O HOH A 433 O HOH A 442 1.87 REMARK 500 OD1 ASN A 244 O HOH A 499 1.88 REMARK 500 N THR A 246 O HOH A 499 1.88 REMARK 500 NZ LYS A 10 O HOH A 418 1.97 REMARK 500 ND2 ASN A 244 O HOH A 438 1.97 REMARK 500 CG1 ILE B 156 O HOH B 547 1.98 REMARK 500 O LYS A 255 O HOH A 580 2.06 REMARK 500 O SER A 265 O HOH A 439 2.07 REMARK 500 OH TYR B 35 O HOH B 687 2.07 REMARK 500 N LYS A 267 O HOH A 439 2.08 REMARK 500 OH TYR B 214 O HOH B 576 2.09 REMARK 500 CE LYS A 10 O HOH A 418 2.10 REMARK 500 O HOH A 494 O HOH A 535 2.11 REMARK 500 OH TYR A 253 O HOH A 603 2.12 REMARK 500 O PRO A 251 O HOH A 584 2.12 REMARK 500 O HOH A 474 O HOH B 570 2.12 REMARK 500 O HOH B 452 O HOH B 599 2.12 REMARK 500 O HOH A 479 O HOH A 573 2.13 REMARK 500 O HOH B 543 O HOH B 561 2.17 REMARK 500 OE1 GLU B 172 O HOH B 592 2.18 REMARK 500 OD1 ASN B 169 O HOH B 643 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 HOH B 475 O HOH B 658 2656 1.95 REMARK 500 O HOH A 609 O HOH B 684 1454 2.02 REMARK 500 O HOH A 417 O HOH B 574 2646 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 102 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 117 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 241 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES 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 LYS A 233 34.11 -96.38 REMARK 500 ASP A 236 101.07 -165.68 REMARK 500 THR A 252 8.35 -58.25 REMARK 500 SER A 254 89.01 -165.92 REMARK 500 ASP B 236 104.15 -161.38 REMARK 500 LEU B 247 77.21 -117.73 REMARK 500 SER B 254 93.55 -163.42 REMARK 500 SER B 265 59.67 -142.14 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 287 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 115 OD2 REMARK 620 2 ASN A 120 OD1 158.5 REMARK 620 3 ASP A 152 OD1 84.5 84.1 REMARK 620 4 HOH A 332 O 87.1 73.1 80.7 REMARK 620 5 HOH A 371 O 93.9 101.5 78.2 158.6 REMARK 620 6 HOH A 376 O 102.7 88.7 172.7 98.4 102.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 288 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 A 289 O4 REMARK 620 2 HOH A 345 O 89.4 REMARK 620 3 HOH A 392 O 83.3 83.4 REMARK 620 4 HOH A 576 O 94.5 172.3 103.6 REMARK 620 5 HOH A 577 O 89.8 89.4 170.0 84.0 REMARK 620 6 HOH A 578 O 167.9 83.6 86.0 93.6 100.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 287 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 115 OD2 REMARK 620 2 ASN B 120 OD1 174.2 REMARK 620 3 ASP B 152 OD1 91.4 87.0 REMARK 620 4 HOH B 299 O 85.8 88.9 97.4 REMARK 620 5 HOH B 302 O 94.3 88.4 167.8 93.8 REMARK 620 6 HOH B 349 O 91.5 93.9 85.3 176.2 83.7 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 MG A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 289 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 288 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WGI RELATED DB: PDB REMARK 900 RELATED ID: 1E9G RELATED DB: PDB REMARK 900 RELATED ID: 1E6A RELATED DB: PDB REMARK 900 RELATED ID: 2IHP RELATED DB: PDB REMARK 900 RELATED ID: 2IK1 RELATED DB: PDB REMARK 900 RELATED ID: 2IK2 RELATED DB: PDB REMARK 900 RELATED ID: 2IK4 RELATED DB: PDB REMARK 900 RELATED ID: 2IK6 RELATED DB: PDB REMARK 900 RELATED ID: 2IK0 RELATED DB: PDB REMARK 900 RELATED ID: 2IK9 RELATED DB: PDB DBREF 2IK7 A 1 286 UNP P00817 IPYR_YEAST 1 286 DBREF 2IK7 B 1 286 UNP P00817 IPYR_YEAST 1 286 SEQADV 2IK7 ASN A 120 UNP P00817 ASP 120 ENGINEERED MUTATION SEQADV 2IK7 ASN B 120 UNP P00817 ASP 120 ENGINEERED MUTATION SEQRES 1 A 286 THR TYR THR THR ARG GLN ILE GLY ALA LYS ASN THR LEU SEQRES 2 A 286 GLU TYR LYS VAL TYR ILE GLU LYS ASP GLY LYS PRO VAL SEQRES 3 A 286 SER ALA PHE HIS ASP ILE PRO LEU TYR ALA ASP LYS GLU SEQRES 4 A 286 ASN ASN ILE PHE ASN MET VAL VAL GLU ILE PRO ARG TRP SEQRES 5 A 286 THR ASN ALA LYS LEU GLU ILE THR LYS GLU GLU THR LEU SEQRES 6 A 286 ASN PRO ILE ILE GLN ASP THR LYS LYS GLY LYS LEU ARG SEQRES 7 A 286 PHE VAL ARG ASN CYS PHE PRO HIS HIS GLY TYR ILE HIS SEQRES 8 A 286 ASN TYR GLY ALA PHE PRO GLN THR TRP GLU ASP PRO ASN SEQRES 9 A 286 VAL SER HIS PRO GLU THR LYS ALA VAL GLY ASP ASN ASP SEQRES 10 A 286 PRO ILE ASN VAL LEU GLU ILE GLY GLU THR ILE ALA TYR SEQRES 11 A 286 THR GLY GLN VAL LYS GLN VAL LYS ALA LEU GLY ILE MET SEQRES 12 A 286 ALA LEU LEU ASP GLU GLY GLU THR ASP TRP LYS VAL ILE SEQRES 13 A 286 ALA ILE ASP ILE ASN ASP PRO LEU ALA PRO LYS LEU ASN SEQRES 14 A 286 ASP ILE GLU ASP VAL GLU LYS TYR PHE PRO GLY LEU LEU SEQRES 15 A 286 ARG ALA THR ASN GLU TRP PHE ARG ILE TYR LYS ILE PRO SEQRES 16 A 286 ASP GLY LYS PRO GLU ASN GLN PHE ALA PHE SER GLY GLU SEQRES 17 A 286 ALA LYS ASN LYS LYS TYR ALA LEU ASP ILE ILE LYS GLU SEQRES 18 A 286 THR HIS ASP SER TRP LYS GLN LEU ILE ALA GLY LYS SER SEQRES 19 A 286 SER ASP SER LYS GLY ILE ASP LEU THR ASN VAL THR LEU SEQRES 20 A 286 PRO ASP THR PRO THR TYR SER LYS ALA ALA SER ASP ALA SEQRES 21 A 286 ILE PRO PRO ALA SER LEU LYS ALA ASP ALA PRO ILE ASP SEQRES 22 A 286 LYS SER ILE ASP LYS TRP PHE PHE ILE SER GLY SER VAL SEQRES 1 B 286 THR TYR THR THR ARG GLN ILE GLY ALA LYS ASN THR LEU SEQRES 2 B 286 GLU TYR LYS VAL TYR ILE GLU LYS ASP GLY LYS PRO VAL SEQRES 3 B 286 SER ALA PHE HIS ASP ILE PRO LEU TYR ALA ASP LYS GLU SEQRES 4 B 286 ASN ASN ILE PHE ASN MET VAL VAL GLU ILE PRO ARG TRP SEQRES 5 B 286 THR ASN ALA LYS LEU GLU ILE THR LYS GLU GLU THR LEU SEQRES 6 B 286 ASN PRO ILE ILE GLN ASP THR LYS LYS GLY LYS LEU ARG SEQRES 7 B 286 PHE VAL ARG ASN CYS PHE PRO HIS HIS GLY TYR ILE HIS SEQRES 8 B 286 ASN TYR GLY ALA PHE PRO GLN THR TRP GLU ASP PRO ASN SEQRES 9 B 286 VAL SER HIS PRO GLU THR LYS ALA VAL GLY ASP ASN ASP SEQRES 10 B 286 PRO ILE ASN VAL LEU GLU ILE GLY GLU THR ILE ALA TYR SEQRES 11 B 286 THR GLY GLN VAL LYS GLN VAL LYS ALA LEU GLY ILE MET SEQRES 12 B 286 ALA LEU LEU ASP GLU GLY GLU THR ASP TRP LYS VAL ILE SEQRES 13 B 286 ALA ILE ASP ILE ASN ASP PRO LEU ALA PRO LYS LEU ASN SEQRES 14 B 286 ASP ILE GLU ASP VAL GLU LYS TYR PHE PRO GLY LEU LEU SEQRES 15 B 286 ARG ALA THR ASN GLU TRP PHE ARG ILE TYR LYS ILE PRO SEQRES 16 B 286 ASP GLY LYS PRO GLU ASN GLN PHE ALA PHE SER GLY GLU SEQRES 17 B 286 ALA LYS ASN LYS LYS TYR ALA LEU ASP ILE ILE LYS GLU SEQRES 18 B 286 THR HIS ASP SER TRP LYS GLN LEU ILE ALA GLY LYS SER SEQRES 19 B 286 SER ASP SER LYS GLY ILE ASP LEU THR ASN VAL THR LEU SEQRES 20 B 286 PRO ASP THR PRO THR TYR SER LYS ALA ALA SER ASP ALA SEQRES 21 B 286 ILE PRO PRO ALA SER LEU LYS ALA ASP ALA PRO ILE ASP SEQRES 22 B 286 LYS SER ILE ASP LYS TRP PHE PHE ILE SER GLY SER VAL HET MG A 287 1 HET MG A 288 1 HET PO4 A 289 5 HET MG B 287 1 HET PO4 B 288 5 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 MG 3(MG 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 8 HOH *736(H2 O) HELIX 1 1 LYS A 38 ASN A 40 5 3 HELIX 2 2 LEU A 164 LEU A 168 5 5 HELIX 3 3 ASP A 170 PHE A 178 1 9 HELIX 4 4 GLY A 180 TYR A 192 1 13 HELIX 5 5 PHE A 205 GLU A 208 5 4 HELIX 6 6 ASN A 211 ALA A 231 1 21 HELIX 7 7 ALA A 256 ILE A 261 1 6 HELIX 8 8 ASP A 273 ASP A 277 5 5 HELIX 9 9 LYS B 38 ASN B 40 5 3 HELIX 10 10 LEU B 164 LEU B 168 5 5 HELIX 11 11 ASP B 170 PHE B 178 1 9 HELIX 12 12 GLY B 180 TYR B 192 1 13 HELIX 13 13 LYS B 193 GLY B 197 5 5 HELIX 14 14 PHE B 205 GLU B 208 5 4 HELIX 15 15 LYS B 212 ALA B 231 1 20 HELIX 16 16 SER B 254 ILE B 261 5 8 HELIX 17 17 ASP B 273 ASP B 277 5 5 SHEET 1 A 3 TYR A 2 ILE A 7 0 SHEET 2 A 3 LYS A 16 LYS A 21 -1 O LYS A 16 N ILE A 7 SHEET 3 A 3 LYS A 24 VAL A 26 -1 O VAL A 26 N ILE A 19 SHEET 1 B 4 TYR A 2 ILE A 7 0 SHEET 2 B 4 LYS A 16 LYS A 21 -1 O LYS A 16 N ILE A 7 SHEET 3 B 4 ILE A 68 GLN A 70 -1 O ILE A 68 N VAL A 17 SHEET 4 B 4 LEU A 57 ILE A 59 -1 N GLU A 58 O ILE A 69 SHEET 1 C 7 TYR A 35 ASP A 37 0 SHEET 2 C 7 ILE A 42 ILE A 49 -1 O ILE A 42 N ALA A 36 SHEET 3 C 7 ASN A 92 ALA A 95 -1 O TYR A 93 N ILE A 49 SHEET 4 C 7 ASN A 120 GLU A 123 -1 O GLU A 123 N ASN A 92 SHEET 5 C 7 GLU A 150 ASP A 159 1 O VAL A 155 N LEU A 122 SHEET 6 C 7 VAL A 134 ASP A 147 -1 N LEU A 140 O ILE A 156 SHEET 7 C 7 GLN A 202 PHE A 203 -1 O GLN A 202 N LEU A 146 SHEET 1 D 4 TYR A 35 ASP A 37 0 SHEET 2 D 4 ILE A 42 ILE A 49 -1 O ILE A 42 N ALA A 36 SHEET 3 D 4 VAL A 134 ASP A 147 -1 O LYS A 135 N MET A 45 SHEET 4 D 4 GLN A 202 PHE A 203 -1 O GLN A 202 N LEU A 146 SHEET 1 E 2 THR A 72 LYS A 73 0 SHEET 2 E 2 LYS A 76 LEU A 77 -1 O LYS A 76 N LYS A 73 SHEET 1 F 2 ASN A 82 CYS A 83 0 SHEET 2 F 2 TRP A 279 PHE A 280 1 O PHE A 280 N ASN A 82 SHEET 1 G 4 LYS B 24 VAL B 26 0 SHEET 2 G 4 LYS B 16 LYS B 21 -1 N ILE B 19 O VAL B 26 SHEET 3 G 4 TYR B 2 GLY B 8 -1 N THR B 3 O GLU B 20 SHEET 4 G 4 SER B 265 LEU B 266 1 O SER B 265 N GLN B 6 SHEET 1 H 7 TYR B 35 ASP B 37 0 SHEET 2 H 7 ILE B 42 ILE B 49 -1 O ILE B 42 N ALA B 36 SHEET 3 H 7 ASN B 92 ALA B 95 -1 O TYR B 93 N ILE B 49 SHEET 4 H 7 ASN B 120 GLU B 123 -1 O GLU B 123 N ASN B 92 SHEET 5 H 7 GLU B 150 ASP B 159 1 O VAL B 155 N LEU B 122 SHEET 6 H 7 VAL B 134 ASP B 147 -1 N LEU B 140 O ILE B 156 SHEET 7 H 7 LYS B 210 ASN B 211 -1 O LYS B 210 N ILE B 142 SHEET 1 I 7 TYR B 35 ASP B 37 0 SHEET 2 I 7 ILE B 42 ILE B 49 -1 O ILE B 42 N ALA B 36 SHEET 3 I 7 ASN B 92 ALA B 95 -1 O TYR B 93 N ILE B 49 SHEET 4 I 7 ASN B 120 GLU B 123 -1 O GLU B 123 N ASN B 92 SHEET 5 I 7 GLU B 150 ASP B 159 1 O VAL B 155 N LEU B 122 SHEET 6 I 7 VAL B 134 ASP B 147 -1 N LEU B 140 O ILE B 156 SHEET 7 I 7 GLN B 202 PHE B 203 -1 O GLN B 202 N LEU B 146 SHEET 1 J 4 TYR B 35 ASP B 37 0 SHEET 2 J 4 ILE B 42 ILE B 49 -1 O ILE B 42 N ALA B 36 SHEET 3 J 4 VAL B 134 ASP B 147 -1 O LYS B 135 N MET B 45 SHEET 4 J 4 GLN B 202 PHE B 203 -1 O GLN B 202 N LEU B 146 SHEET 1 K 4 TYR B 35 ASP B 37 0 SHEET 2 K 4 ILE B 42 ILE B 49 -1 O ILE B 42 N ALA B 36 SHEET 3 K 4 VAL B 134 ASP B 147 -1 O LYS B 135 N MET B 45 SHEET 4 K 4 LYS B 210 ASN B 211 -1 O LYS B 210 N ILE B 142 SHEET 1 L 2 LEU B 57 ILE B 59 0 SHEET 2 L 2 ILE B 68 GLN B 70 -1 O ILE B 69 N GLU B 58 SHEET 1 M 2 THR B 72 LYS B 73 0 SHEET 2 M 2 LYS B 76 LEU B 77 -1 O LYS B 76 N LYS B 73 SHEET 1 N 2 ASN B 82 CYS B 83 0 SHEET 2 N 2 TRP B 279 PHE B 280 1 O PHE B 280 N ASN B 82 LINK OD2 ASP A 115 MG MG A 287 1555 1555 2.04 LINK OD1 ASN A 120 MG MG A 287 1555 1555 2.23 LINK OD1 ASP A 152 MG MG A 287 1555 1555 2.36 LINK MG MG A 287 O HOH A 332 1555 1555 1.86 LINK MG MG A 287 O HOH A 371 1555 1555 2.30 LINK MG MG A 287 O HOH A 376 1555 1555 2.02 LINK MG MG A 288 O4 PO4 A 289 1555 1555 1.92 LINK MG MG A 288 O HOH A 345 1555 1555 2.28 LINK MG MG A 288 O HOH A 392 1555 1555 2.04 LINK MG MG A 288 O HOH A 576 1555 1555 2.24 LINK MG MG A 288 O HOH A 577 1555 1555 2.09 LINK MG MG A 288 O HOH A 578 1555 1555 2.06 LINK OD2 ASP B 115 MG MG B 287 1555 1555 2.16 LINK OD1 ASN B 120 MG MG B 287 1555 1555 2.14 LINK OD1 ASP B 152 MG MG B 287 1555 1555 2.19 LINK MG MG B 287 O HOH B 299 1555 1555 2.08 LINK MG MG B 287 O HOH B 302 1555 1555 2.24 LINK MG MG B 287 O HOH B 349 1555 1555 2.21 CISPEP 1 PHE A 84 PRO A 85 0 4.02 CISPEP 2 PHE B 84 PRO B 85 0 0.32 SITE 1 AC1 6 ASP A 115 ASN A 120 ASP A 152 HOH A 332 SITE 2 AC1 6 HOH A 371 HOH A 376 SITE 1 AC2 6 PO4 A 289 HOH A 345 HOH A 392 HOH A 576 SITE 2 AC2 6 HOH A 577 HOH A 578 SITE 1 AC3 6 ASP B 115 ASN B 120 ASP B 152 HOH B 299 SITE 2 AC3 6 HOH B 302 HOH B 349 SITE 1 AC4 13 ARG A 78 ASP A 147 TYR A 192 LYS A 193 SITE 2 AC4 13 MG A 288 HOH A 345 HOH A 366 HOH A 367 SITE 3 AC4 13 HOH A 371 HOH A 392 HOH A 428 HOH A 576 SITE 4 AC4 13 HOH A 577 SITE 1 AC5 10 LYS B 56 ARG B 78 ASP B 147 TYR B 192 SITE 2 AC5 10 LYS B 193 HOH B 338 HOH B 347 HOH B 349 SITE 3 AC5 10 HOH B 673 HOH B 690 CRYST1 51.652 93.000 69.266 90.00 99.33 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 0.019360 0.000000 0.003180 0.00000 SCALE2 0.000000 0.010753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014631 0.00000