HEADER HYDROLASE 09-JUN-05 1ZY9 TITLE CRYSTAL STRUCTURE OF ALPHA-GALACTOSIDASE (EC 3.2.1.22) (MELIBIASE) TITLE 2 (TM1192) FROM THERMOTOGA MARITIMA AT 2.34 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM1192; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TM1192, ALPHA-GALACTOSIDASE (EC 3.2.1.22) (MELIBIASE), STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 16-OCT-24 1ZY9 1 REMARK REVDAT 4 25-JAN-23 1ZY9 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1ZY9 1 VERSN REVDAT 2 24-FEB-09 1ZY9 1 VERSN REVDAT 1 12-JUL-05 1ZY9 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF ALPHA-GALACTOSIDASE (EC 3.2.1.22) JRNL TITL 2 (MELIBIASE) (TM1192) FROM THERMOTOGA MARITIMA AT 2.34 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 34093 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1792 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2559 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -1.99000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.837 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4397 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3954 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5970 ; 1.550 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9198 ; 0.812 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 535 ; 7.102 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;35.948 ;24.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 732 ;15.633 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.758 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 638 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4881 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 919 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 839 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4137 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2130 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2672 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 214 ; 0.167 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.108 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 25 ; 0.175 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.137 ; 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): 2841 ; 2.588 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1066 ; 0.508 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4284 ; 3.324 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1997 ; 5.917 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1682 ; 7.690 ;11.000 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 : 1.20 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. THE DENSITY BLOB BETWEEN SIDE CHAINS OF A220,A387 IS REMARK 3 TENATIVELY MODELED AS A GLYCEROL. REMARK 4 REMARK 4 1ZY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979413, 0.918370, 0.979170 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : FLAT MIRROR, SIDE-DEFELECTING REMARK 200 MONOCHROMATOR (SI 111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35967 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 42.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : 0.12900 REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.60300 REMARK 200 R SYM FOR SHELL (I) : 0.60300 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M K3CIRTRATE, 20.0% PEG-3350, NO REMARK 280 BUFFER, PH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, REMARK 280 TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 44.12900 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 44.12900 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 60.86450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.26650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.86450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.26650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.12900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.86450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.26650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.12900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.86450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 80.26650 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 MSE A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 526 REMARK 465 LYS A 527 REMARK 465 SER A 528 REMARK 465 SER A 529 REMARK 465 LEU A 530 REMARK 465 LYS A 531 REMARK 465 LYS A 532 REMARK 465 ARG A 533 REMARK 465 VAL A 534 REMARK 465 VAL A 535 REMARK 465 LYS A 536 REMARK 465 ARG A 537 REMARK 465 GLU A 538 REMARK 465 ASP A 539 REMARK 465 GLY A 540 REMARK 465 ARG A 541 REMARK 465 ASN A 542 REMARK 465 PHE A 543 REMARK 465 TYR A 544 REMARK 465 PHE A 545 REMARK 465 TYR A 546 REMARK 465 GLU A 547 REMARK 465 GLU A 548 REMARK 465 GLY A 549 REMARK 465 GLU A 550 REMARK 465 ARG A 551 REMARK 465 GLU A 552 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 9 CZ NH1 NH2 REMARK 470 ARG A 12 CZ NH1 NH2 REMARK 470 LYS A 18 CE NZ REMARK 470 GLU A 27 CD OE1 OE2 REMARK 470 LYS A 77 CD CE NZ REMARK 470 GLU A 80 CD OE1 OE2 REMARK 470 LYS A 181 CD CE NZ REMARK 470 LYS A 207 CD CE NZ REMARK 470 ARG A 234 NH1 NH2 REMARK 470 LYS A 245 NZ REMARK 470 GLU A 272 OE1 OE2 REMARK 470 LYS A 318 CE NZ REMARK 470 LYS A 357 NZ REMARK 470 LYS A 475 CD CE NZ REMARK 470 ARG A 496 CZ NH1 NH2 REMARK 470 GLU A 525 CG CD OE1 OE2 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 OD1 ASP A 425 O HOH A 592 2.15 REMARK 500 OH TYR A 113 O HOH A 684 2.15 REMARK 500 O HOH A 667 O HOH A 682 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 378 CB CYS A 378 SG -0.116 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 TRP A 85 35.66 -140.01 REMARK 500 TYR A 104 -47.67 80.41 REMARK 500 ASP A 157 144.49 -179.97 REMARK 500 PHE A 194 -132.95 46.91 REMARK 500 ALA A 222 -34.49 152.19 REMARK 500 ASP A 229 73.51 -112.40 REMARK 500 ASP A 236 -35.25 -35.96 REMARK 500 SER A 239 143.55 -30.27 REMARK 500 ALA A 259 72.86 -109.82 REMARK 500 LEU A 372 -73.33 -81.23 REMARK 500 CYS A 378 -49.59 -132.01 REMARK 500 PRO A 390 36.78 -77.62 REMARK 500 ARG A 420 -51.89 -134.17 REMARK 500 TRP A 422 -175.33 161.23 REMARK 500 ASP A 427 160.65 75.55 REMARK 500 ARG A 467 -150.56 -123.87 REMARK 500 ASN A 489 60.07 -119.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 553 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 556 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 557 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283057 RELATED DB: TARGETDB DBREF 1ZY9 A 1 552 UNP O33835 O33835_THEMA 1 552 SEQADV 1ZY9 MSE A -11 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 GLY A -10 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 SER A -9 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 ASP A -8 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 LYS A -7 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 ILE A -6 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A -5 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A -4 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A -3 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A -2 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A -1 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 HIS A 0 UNP O33835 EXPRESSION TAG SEQADV 1ZY9 MSE A 1 UNP O33835 MET 1 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 173 UNP O33835 MET 173 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 243 UNP O33835 MET 243 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 286 UNP O33835 MET 286 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 319 UNP O33835 MET 319 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 382 UNP O33835 MET 382 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 417 UNP O33835 MET 417 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 456 UNP O33835 MET 456 MODIFIED RESIDUE SEQADV 1ZY9 MSE A 491 UNP O33835 MET 491 MODIFIED RESIDUE SEQRES 1 A 564 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 564 GLU ILE PHE GLY LYS THR PHE ARG GLU GLY ARG PHE VAL SEQRES 3 A 564 LEU LYS GLU LYS ASN PHE THR VAL GLU PHE ALA VAL GLU SEQRES 4 A 564 LYS ILE HIS LEU GLY TRP LYS ILE SER GLY ARG VAL LYS SEQRES 5 A 564 GLY SER PRO GLY ARG LEU GLU VAL LEU ARG THR LYS ALA SEQRES 6 A 564 PRO GLU LYS VAL LEU VAL ASN ASN TRP GLN SER TRP GLY SEQRES 7 A 564 PRO CYS ARG VAL VAL ASP ALA PHE SER PHE LYS PRO PRO SEQRES 8 A 564 GLU ILE ASP PRO ASN TRP ARG TYR THR ALA SER VAL VAL SEQRES 9 A 564 PRO ASP VAL LEU GLU ARG ASN LEU GLN SER ASP TYR PHE SEQRES 10 A 564 VAL ALA GLU GLU GLY LYS VAL TYR GLY PHE LEU SER SER SEQRES 11 A 564 LYS ILE ALA HIS PRO PHE PHE ALA VAL GLU ASP GLY GLU SEQRES 12 A 564 LEU VAL ALA TYR LEU GLU TYR PHE ASP VAL GLU PHE ASP SEQRES 13 A 564 ASP PHE VAL PRO LEU GLU PRO LEU VAL VAL LEU GLU ASP SEQRES 14 A 564 PRO ASN THR PRO LEU LEU LEU GLU LYS TYR ALA GLU LEU SEQRES 15 A 564 VAL GLY MSE GLU ASN ASN ALA ARG VAL PRO LYS HIS THR SEQRES 16 A 564 PRO THR GLY TRP CYS SER TRP TYR HIS TYR PHE LEU ASP SEQRES 17 A 564 LEU THR TRP GLU GLU THR LEU LYS ASN LEU LYS LEU ALA SEQRES 18 A 564 LYS ASN PHE PRO PHE GLU VAL PHE GLN ILE ASP ASP ALA SEQRES 19 A 564 TYR GLU LYS ASP ILE GLY ASP TRP LEU VAL THR ARG GLY SEQRES 20 A 564 ASP PHE PRO SER VAL GLU GLU MSE ALA LYS VAL ILE ALA SEQRES 21 A 564 GLU ASN GLY PHE ILE PRO GLY ILE TRP THR ALA PRO PHE SEQRES 22 A 564 SER VAL SER GLU THR SER ASP VAL PHE ASN GLU HIS PRO SEQRES 23 A 564 ASP TRP VAL VAL LYS GLU ASN GLY GLU PRO LYS MSE ALA SEQRES 24 A 564 TYR ARG ASN TRP ASN LYS LYS ILE TYR ALA LEU ASP LEU SEQRES 25 A 564 SER LYS ASP GLU VAL LEU ASN TRP LEU PHE ASP LEU PHE SEQRES 26 A 564 SER SER LEU ARG LYS MSE GLY TYR ARG TYR PHE LYS ILE SEQRES 27 A 564 ASP PHE LEU PHE ALA GLY ALA VAL PRO GLY GLU ARG LYS SEQRES 28 A 564 LYS ASN ILE THR PRO ILE GLN ALA PHE ARG LYS GLY ILE SEQRES 29 A 564 GLU THR ILE ARG LYS ALA VAL GLY GLU ASP SER PHE ILE SEQRES 30 A 564 LEU GLY CYS GLY SER PRO LEU LEU PRO ALA VAL GLY CYS SEQRES 31 A 564 VAL ASP GLY MSE ARG ILE GLY PRO ASP THR ALA PRO PHE SEQRES 32 A 564 TRP GLY GLU HIS ILE GLU ASP ASN GLY ALA PRO ALA ALA SEQRES 33 A 564 ARG TRP ALA LEU ARG ASN ALA ILE THR ARG TYR PHE MSE SEQRES 34 A 564 HIS ASP ARG PHE TRP LEU ASN ASP PRO ASP CYS LEU ILE SEQRES 35 A 564 LEU ARG GLU GLU LYS THR ASP LEU THR GLN LYS GLU LYS SEQRES 36 A 564 GLU LEU TYR SER TYR THR CYS GLY VAL LEU ASP ASN MSE SEQRES 37 A 564 ILE ILE GLU SER ASP ASP LEU SER LEU VAL ARG ASP HIS SEQRES 38 A 564 GLY LYS LYS VAL LEU LYS GLU THR LEU GLU LEU LEU GLY SEQRES 39 A 564 GLY ARG PRO ARG VAL GLN ASN ILE MSE SER GLU ASP LEU SEQRES 40 A 564 ARG TYR GLU ILE VAL SER SER GLY THR LEU SER GLY ASN SEQRES 41 A 564 VAL LYS ILE VAL VAL ASP LEU ASN SER ARG GLU TYR HIS SEQRES 42 A 564 LEU GLU LYS GLU GLY LYS SER SER LEU LYS LYS ARG VAL SEQRES 43 A 564 VAL LYS ARG GLU ASP GLY ARG ASN PHE TYR PHE TYR GLU SEQRES 44 A 564 GLU GLY GLU ARG GLU MODRES 1ZY9 MSE A 1 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 173 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 243 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 286 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 319 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 382 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 417 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 456 MET SELENOMETHIONINE MODRES 1ZY9 MSE A 491 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 173 8 HET MSE A 243 8 HET MSE A 286 8 HET MSE A 319 8 HET MSE A 382 8 HET MSE A 417 8 HET MSE A 456 8 HET MSE A 491 8 HET EDO A 553 4 HET EDO A 554 4 HET EDO A 555 4 HET EDO A 556 4 HET GOL A 557 6 HETNAM MSE SELENOMETHIONINE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *244(H2 O) HELIX 1 1 PHE A 74 PHE A 76 5 3 HELIX 2 2 ASP A 82 ASN A 84 5 3 HELIX 3 3 TRP A 85 SER A 90 1 6 HELIX 4 4 VAL A 92 GLU A 97 1 6 HELIX 5 5 ASN A 159 ASN A 175 1 17 HELIX 6 6 SER A 189 PHE A 194 1 6 HELIX 7 7 LEU A 195 LEU A 197 5 3 HELIX 8 8 THR A 198 ALA A 209 1 12 HELIX 9 9 LYS A 210 PHE A 212 5 3 HELIX 10 10 SER A 239 ASN A 250 1 12 HELIX 11 11 SER A 267 HIS A 273 1 7 HELIX 12 12 PRO A 274 VAL A 277 5 4 HELIX 13 13 LYS A 302 MSE A 319 1 18 HELIX 14 14 PHE A 328 VAL A 334 5 7 HELIX 15 15 THR A 343 GLY A 360 1 18 HELIX 16 16 LEU A 372 VAL A 376 5 5 HELIX 17 17 ALA A 403 ARG A 414 1 12 HELIX 18 18 TYR A 415 HIS A 418 5 4 HELIX 19 19 THR A 439 LEU A 453 1 15 HELIX 20 20 ASP A 462 VAL A 466 5 5 HELIX 21 21 ARG A 467 GLU A 479 1 13 SHEET 1 A 6 LYS A 6 THR A 7 0 SHEET 2 A 6 MSE A 1 ILE A 3 -1 N ILE A 3 O LYS A 6 SHEET 3 A 6 ARG A 45 LYS A 52 -1 O ARG A 50 N GLU A 2 SHEET 4 A 6 GLU A 131 GLU A 137 -1 O LEU A 132 N THR A 51 SHEET 5 A 6 HIS A 122 GLU A 128 -1 N PHE A 124 O TYR A 135 SHEET 6 A 6 LEU A 100 ASP A 103 -1 N SER A 102 O PHE A 125 SHEET 1 B 6 GLY A 11 LYS A 16 0 SHEET 2 B 6 PHE A 20 ILE A 29 -1 O VAL A 26 N GLY A 11 SHEET 3 B 6 GLY A 32 GLY A 41 -1 O LYS A 34 N GLU A 27 SHEET 4 B 6 LEU A 152 GLU A 156 -1 O LEU A 152 N ILE A 35 SHEET 5 B 6 LYS A 111 PHE A 115 -1 N GLY A 114 O VAL A 153 SHEET 6 B 6 PHE A 105 GLU A 108 -1 N VAL A 106 O TYR A 113 SHEET 1 C 4 GLY A 11 LYS A 16 0 SHEET 2 C 4 PHE A 20 ILE A 29 -1 O VAL A 26 N GLY A 11 SHEET 3 C 4 GLY A 32 GLY A 41 -1 O LYS A 34 N GLU A 27 SHEET 4 C 4 PHE A 143 PRO A 148 -1 O VAL A 147 N VAL A 39 SHEET 1 D 2 LYS A 56 ASN A 60 0 SHEET 2 D 2 CYS A 68 ASP A 72 -1 O ARG A 69 N VAL A 59 SHEET 1 E 8 LEU A 423 ASP A 425 0 SHEET 2 E 8 GLY A 381 ARG A 383 1 N MSE A 382 O ASP A 425 SHEET 3 E 8 PHE A 364 GLY A 367 1 N GLY A 367 O GLY A 381 SHEET 4 E 8 TYR A 323 ILE A 326 1 N PHE A 324 O LEU A 366 SHEET 5 E 8 ILE A 253 THR A 258 1 N THR A 258 O LYS A 325 SHEET 6 E 8 VAL A 216 ILE A 219 1 N PHE A 217 O ILE A 253 SHEET 7 E 8 THR A 185 CYS A 188 1 N TRP A 187 O GLN A 218 SHEET 8 E 8 ILE A 457 GLU A 459 1 O GLU A 459 N GLY A 186 SHEET 1 F 3 SER A 262 SER A 264 0 SHEET 2 F 3 LYS A 293 ALA A 297 -1 O TYR A 296 N VAL A 263 SHEET 3 F 3 MSE A 286 ASN A 290 -1 N TYR A 288 O ILE A 295 SHEET 1 G 2 LYS A 279 GLU A 280 0 SHEET 2 G 2 GLU A 283 PRO A 284 -1 O GLU A 283 N GLU A 280 SHEET 1 H 4 ARG A 484 VAL A 487 0 SHEET 2 H 4 ARG A 496 THR A 504 -1 O VAL A 500 N ARG A 486 SHEET 3 H 4 GLY A 507 ASP A 514 -1 O ILE A 511 N ILE A 499 SHEET 4 H 4 GLU A 519 GLU A 523 -1 O HIS A 521 N VAL A 512 LINK C HIS A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N GLU A 2 1555 1555 1.33 LINK C GLY A 172 N MSE A 173 1555 1555 1.32 LINK C MSE A 173 N GLU A 174 1555 1555 1.33 LINK C GLU A 242 N MSE A 243 1555 1555 1.32 LINK C MSE A 243 N ALA A 244 1555 1555 1.32 LINK C LYS A 285 N MSE A 286 1555 1555 1.32 LINK C MSE A 286 N ALA A 287 1555 1555 1.33 LINK C LYS A 318 N MSE A 319 1555 1555 1.33 LINK C MSE A 319 N GLY A 320 1555 1555 1.33 LINK C GLY A 381 N MSE A 382 1555 1555 1.32 LINK C MSE A 382 N ARG A 383 1555 1555 1.33 LINK C PHE A 416 N MSE A 417 1555 1555 1.32 LINK C MSE A 417 N HIS A 418 1555 1555 1.33 LINK C ASN A 455 N MSE A 456 1555 1555 1.32 LINK C MSE A 456 N ILE A 457 1555 1555 1.33 LINK C ILE A 490 N MSE A 491 1555 1555 1.34 LINK C MSE A 491 N SER A 492 1555 1555 1.33 SITE 1 AC1 7 ILE A 3 LYS A 6 THR A 7 PHE A 8 SITE 2 AC1 7 ARG A 9 PHE A 13 PHE A 24 SITE 1 AC2 6 TRP A 65 PRO A 386 ASP A 387 GLY A 400 SITE 2 AC2 6 ALA A 401 PRO A 402 SITE 1 AC3 2 TRP A 65 GLY A 400 SITE 1 AC4 4 ASN A 290 TRP A 291 HOH A 597 HOH A 692 SITE 1 AC5 8 TRP A 190 TYR A 191 ASP A 220 TRP A 257 SITE 2 AC5 8 LYS A 325 ASP A 327 ARG A 383 ASP A 387 CRYST1 121.729 160.533 88.258 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008210 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011330 0.00000