PDB Short entry for 4HA4 HEADER HYDROLASE 25-SEP-12 4HA4 TITLE STRUCTURE OF BETA-GLYCOSIDASE FROM ACIDILOBUS SACCHAROVORANS IN TITLE 2 COMPLEX WITH GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.23; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDILOBUS SACCHAROVORANS; SOURCE 3 ORGANISM_TAXID: 666510; SOURCE 4 STRAIN: DSM 16705 / VKM B-2471 / 345-15; SOURCE 5 GENE: ASAC1390, ASAC_1390; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DLT1270 (PRARE2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS TIM BARREL, BETA-GLYCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.TROFIMOV,K.M.POLYAKOV,A.V.TIKHONOV,E.Y.BEZSUDNOVA, AUTHOR 2 P.V.DOROVATOVSKII,V.M.GUMEROV,N.V.RAVIN,K.G.SKRYABIN,V.O.POPOV REVDAT 3 04-SEP-13 4HA4 1 JRNL REVDAT 2 17-OCT-12 4HA4 1 AUTHOR TITLE REVDAT 1 10-OCT-12 4HA4 0 JRNL AUTH A.A.TROFIMOV,K.M.POLYAKOV,A.V.TIKHONOV,E.Y.BEZSUDNOVA, JRNL AUTH 2 P.V.DOROVATOVSKII,V.M.GUMEROV,N.V.RAVIN,K.G.SKRYABIN, JRNL AUTH 3 V.O.POPOV JRNL TITL STRUCTURES OF BETA-GLYCOSIDASE FROM ACIDILOBUS JRNL TITL 2 SACCHAROVORANS IN COMPLEXES WITH TRIS AND GLYCEROL. JRNL REF DOKL.BIOCHEM.BIOPHYS. V. 449 99 JRNL REFN ISSN 1607-6729 JRNL PMID 23657657 JRNL DOI 10.1134/S1607672913020129 REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 117803 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6243 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) : 1.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8083 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 432 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 543 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.55000 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): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.533 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4177 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2635 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5654 ; 1.559 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6327 ; 0.927 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 488 ; 6.226 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;32.875 ;22.804 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 633 ;12.343 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.576 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 563 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4659 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 912 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2430 ; 1.478 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 992 ; 0.722 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3916 ; 2.075 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1747 ; 2.945 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1737 ; 3.974 ; 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): 6812 ; 1.387 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 544 ; 7.943 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6697 ; 3.704 ; 3.000 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 4HA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-12. REMARK 100 THE RCSB ID CODE IS RCSB075210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : KURCHATOV SNC REMARK 200 BEAMLINE : K4.4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9815 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 124046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 19.827 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.81000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (1.5MCL): 13MG/ML REMARK 280 ASBETA-GLY, 0.025M NACL, 0.025M HEPES (PH 7.5). RESERVOIR REMARK 280 SOLUTION (1.5MCL): 1.0M SUCCINIC ACID (PH 7.0), 0.1M HEPES (PH REMARK 280 7.0), 1% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000. THE REMARK 280 CRYSTAL WAS SOAKED IN A CRYOPROTECTION SOLUTION CONTAINING 20% V/ REMARK 280 V GLYCEROL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.06000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.13500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.06000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.06000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.13500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.06000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.06000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.13500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.06000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.06000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.13500 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 25.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 -84.12000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -84.12000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 -84.12000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -84.12000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 501 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 876 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 828 LIES ON A SPECIAL POSITION. 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 7 CG CD CE NZ REMARK 470 ARG A 91 NE CZ NH1 NH2 REMARK 470 LYS A 97 CD CE NZ REMARK 470 LYS A 103 CD CE NZ REMARK 470 ARG A 328 NE CZ NH1 NH2 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 SER A 222 CB SER A 222 OG 0.090 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 HIS A 152 40.47 -143.70 REMARK 500 TRP A 153 -55.45 110.42 REMARK 500 ALA A 218 -59.73 -125.32 REMARK 500 CYS A 230 97.01 -166.60 REMARK 500 ARG A 288 -58.01 -137.99 REMARK 500 ARG A 311 47.62 -96.55 REMARK 500 ASP A 390 92.62 -161.46 REMARK 500 TRP A 431 -131.14 57.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1102 DISTANCE = 5.93 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 506 REMARK 610 PG4 A 507 REMARK 610 PG4 A 508 REMARK 610 PG4 A 509 REMARK 610 PG6 A 510 REMARK 610 PG4 A 511 REMARK 610 PG4 A 512 REMARK 610 PG4 A 513 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 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 652 O REMARK 620 2 HOH A 613 O 86.5 REMARK 620 3 ASP A 393 O 80.8 79.3 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 NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG6 A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 513 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HA3 RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-GLYCOSIDASE FROM ACIDILOBUS REMARK 900 SACCHARAVORANS IN COMPLEX WITH TRIS DBREF 4HA4 A 2 490 UNP D9PZ08 D9PZ08_ACIS3 2 490 SEQRES 1 A 489 ALA VAL THR PHE PRO LYS ASP PHE LEU PHE GLY TRP SER SEQRES 2 A 489 GLN ALA GLY PHE GLN SER GLU MET GLY THR PRO GLY SER SEQRES 3 A 489 GLU ASP PRO ASN SER ASP TRP TYR ALA TRP VAL HIS ASP SEQRES 4 A 489 ARG GLU ASN ILE ALA ALA GLY LEU VAL SER GLY ASP PHE SEQRES 5 A 489 PRO GLU ASN GLY PRO GLY TYR TRP GLY ASN TYR ARG LYS SEQRES 6 A 489 PHE HIS ASP ALA ALA GLN ALA MET GLY LEU THR ALA ALA SEQRES 7 A 489 ARG ILE GLY VAL GLU TRP SER ARG ILE PHE PRO ARG PRO SEQRES 8 A 489 THR PHE ASP VAL LYS VAL ASP ALA GLU VAL LYS GLY ASP SEQRES 9 A 489 ASP VAL LEU SER VAL TYR VAL SER GLU GLY ALA LEU GLU SEQRES 10 A 489 GLN LEU ASP LYS MET ALA ASN ARG ASP ALA ILE ASN HIS SEQRES 11 A 489 TYR ARG GLU MET PHE SER ASP LEU ARG SER ARG GLY ILE SEQRES 12 A 489 THR PHE ILE LEU ASN LEU TYR HIS TRP PRO LEU PRO LEU SEQRES 13 A 489 TRP LEU HIS ASP PRO ILE ALA ILE ARG ARG GLY ASN LEU SEQRES 14 A 489 SER ALA PRO SER GLY TRP LEU ASP VAL ARG THR VAL ILE SEQRES 15 A 489 GLU PHE ALA LYS PHE SER ALA TYR VAL ALA TRP LYS LEU SEQRES 16 A 489 ASP ASP LEU VAL TYR MET TYR SER THR MET ASN GLU PRO SEQRES 17 A 489 ASN VAL VAL TRP GLY LEU GLY TYR ALA ALA VAL LYS SER SEQRES 18 A 489 GLY PHE PRO PRO GLY TYR LEU CYS LEU GLU CYS ALA GLY SEQRES 19 A 489 ARG ALA MET LYS ASN LEU VAL GLN ALA HIS ALA ARG ALA SEQRES 20 A 489 TYR ASP ALA VAL LYS ALA ILE THR LYS LYS PRO VAL GLY SEQRES 21 A 489 VAL ILE TYR ALA ASN SER ASP PHE THR PRO LEU THR ASP SEQRES 22 A 489 ALA ASP ARG GLU ALA ALA GLU ARG ALA LYS PHE ASP ASN SEQRES 23 A 489 ARG TRP ALA PHE PHE ASP ALA VAL VAL ARG GLY GLN LEU SEQRES 24 A 489 GLY GLY SER THR ARG ASP ASP LEU LYS GLY ARG LEU ASP SEQRES 25 A 489 TRP ILE GLY VAL ASN TYR TYR THR ARG GLN VAL VAL ARG SEQRES 26 A 489 ALA ARG GLY SER GLY TYR GLU ILE VAL PRO GLY TYR GLY SEQRES 27 A 489 HIS GLY CYS GLU PRO ASN GLY VAL SER PRO ALA GLY ARG SEQRES 28 A 489 PRO CYS SER ASP PHE GLY TRP GLU PHE TYR PRO GLU GLY SEQRES 29 A 489 LEU TYR ASN VAL LEU LYS GLU TYR TRP ASP ARG TYR HIS SEQRES 30 A 489 LEU PRO LEU LEU VAL THR GLU ASN GLY ILE ALA ASP GLU SEQRES 31 A 489 GLY ASP TYR GLN ARG PRO TYR TYR LEU VAL SER HIS VAL SEQRES 32 A 489 TYR GLN VAL HIS ARG ALA LEU GLN ASP GLY VAL ASN VAL SEQRES 33 A 489 ILE GLY TYR LEU HIS TRP SER LEU ALA ASP ASN TYR GLU SEQRES 34 A 489 TRP ALA SER GLY PHE SER LYS ARG PHE GLY LEU LEU MET SEQRES 35 A 489 VAL ASP TYR SER THR LYS ARG LEU HIS TRP ARG PRO SER SEQRES 36 A 489 ALA PHE ILE TYR ARG GLU ILE ALA LYS SER ARG ALA ILE SEQRES 37 A 489 THR ASP GLU ILE GLU HIS LEU ASN SER VAL PRO PRO LEU SEQRES 38 A 489 ARG GLY LEU SER PRO GLY HIS ARG HET NA A 501 1 HET SIN A 502 8 HET GOL A 503 11 HET GOL A 504 7 HET GOL A 505 7 HET PG4 A 506 9 HET PG4 A 507 4 HET PG4 A 508 4 HET PG4 A 509 5 HET PG6 A 510 13 HET PG4 A 511 3 HET PG4 A 512 3 HET PG4 A 513 4 HETNAM NA SODIUM ION HETNAM SIN SUCCINIC ACID HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]- HETNAM 2 PG6 ETHOXY}-ETHANE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NA NA 1+ FORMUL 3 SIN C4 H6 O4 FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 PG4 7(C8 H18 O5) FORMUL 11 PG6 C12 H26 O6 FORMUL 15 HOH *543(H2 O) HELIX 1 1 ALA A 16 GLU A 21 1 6 HELIX 2 2 SER A 32 ASP A 40 1 9 HELIX 3 3 ASP A 40 ALA A 46 1 7 HELIX 4 4 PHE A 53 GLY A 57 5 5 HELIX 5 5 GLY A 59 MET A 74 1 16 HELIX 6 6 GLU A 84 PHE A 89 1 6 HELIX 7 7 SER A 113 ALA A 124 1 12 HELIX 8 8 ASN A 125 ARG A 142 1 18 HELIX 9 9 ASP A 161 ARG A 167 1 7 HELIX 10 10 SER A 174 LEU A 177 5 4 HELIX 11 11 ASP A 178 ASP A 197 1 20 HELIX 12 12 ASP A 198 VAL A 200 5 3 HELIX 13 13 GLU A 208 ALA A 218 1 11 HELIX 14 14 ALA A 219 GLY A 223 5 5 HELIX 15 15 CYS A 230 ALA A 254 1 25 HELIX 16 16 THR A 273 ALA A 275 5 3 HELIX 17 17 ASP A 276 ARG A 288 1 13 HELIX 18 18 ARG A 288 GLY A 298 1 11 HELIX 19 19 PRO A 363 HIS A 378 1 16 HELIX 20 20 GLN A 395 ASP A 413 1 19 HELIX 21 21 GLU A 430 LYS A 437 5 8 HELIX 22 22 ARG A 454 ARG A 467 1 14 HELIX 23 23 ILE A 473 ASN A 477 5 5 SHEET 1 A 2 VAL A 3 THR A 4 0 SHEET 2 A 2 ALA A 468 ILE A 469 -1 O ILE A 469 N VAL A 3 SHEET 1 B10 GLY A 331 ILE A 334 0 SHEET 2 B10 ILE A 315 ARG A 328 -1 N ARG A 326 O GLU A 333 SHEET 3 B10 LEU A 381 GLU A 385 1 O LEU A 382 N VAL A 317 SHEET 4 B10 VAL A 417 HIS A 422 1 O ILE A 418 N LEU A 381 SHEET 5 B10 LEU A 10 GLN A 15 1 N LEU A 10 O TYR A 420 SHEET 6 B10 ALA A 78 GLY A 82 1 O ARG A 80 N TRP A 13 SHEET 7 B10 THR A 145 ASN A 149 1 O ILE A 147 N ALA A 79 SHEET 8 B10 MET A 202 ASN A 207 1 O SER A 204 N LEU A 148 SHEET 9 B10 VAL A 260 PRO A 271 1 O GLY A 261 N TYR A 203 SHEET 10 B10 ILE A 315 ARG A 328 1 O GLY A 316 N VAL A 262 SHEET 1 C 2 ASP A 99 LYS A 103 0 SHEET 2 C 2 ASP A 106 TYR A 111 -1 O LEU A 108 N GLU A 101 SHEET 1 D 2 GLN A 299 LEU A 300 0 SHEET 2 D 2 SER A 303 THR A 304 -1 O SER A 303 N LEU A 300 SHEET 1 E 2 LEU A 442 VAL A 444 0 SHEET 2 E 2 LEU A 451 TRP A 453 -1 O HIS A 452 N MET A 443 SSBOND 1 CYS A 230 CYS A 233 1555 1555 2.09 LINK NA NA A 501 O HOH A 652 1555 1555 2.32 LINK NA NA A 501 O HOH A 613 1555 1555 2.43 LINK O ASP A 393 NA NA A 501 1555 1555 2.57 CISPEP 1 PRO A 225 PRO A 226 0 -4.15 CISPEP 2 TRP A 423 SER A 424 0 4.62 SITE 1 AC1 3 ASP A 393 HOH A 613 HOH A 652 SITE 1 AC2 3 ARG A 461 LYS A 465 HOH A 858 SITE 1 AC3 10 TRP A 153 LEU A 215 PHE A 224 PHE A 357 SITE 2 AC3 10 GLU A 430 TRP A 431 GOL A 505 HOH A 672 SITE 3 AC3 10 HOH A 816 HOH A1077 SITE 1 AC4 8 GLU A 391 ARG A 438 MET A 443 ARG A 454 SITE 2 AC4 8 PRO A 481 HOH A 747 HOH A 820 HOH A1120 SITE 1 AC5 9 GLN A 19 HIS A 152 ASN A 207 GLU A 208 SITE 2 AC5 9 GLU A 385 TRP A 423 GLU A 430 TRP A 431 SITE 3 AC5 9 GOL A 503 SITE 1 AC6 5 ASN A 210 GLY A 214 LEU A 215 GLN A 323 SITE 2 AC6 5 PG4 A 507 SITE 1 AC7 10 ALA A 265 ASN A 266 SER A 267 GLN A 323 SITE 2 AC7 10 HIS A 340 PG4 A 506 HOH A 629 HOH A 693 SITE 3 AC7 10 HOH A 931 HOH A1136 SITE 1 AC8 6 TRP A 374 HIS A 378 LEU A 379 PRO A 380 SITE 2 AC8 6 ASN A 416 HOH A1073 SITE 1 AC9 6 ASN A 63 LYS A 66 LYS A 449 HOH A 647 SITE 2 AC9 6 HOH A 686 HOH A1036 SITE 1 BC1 6 TYR A 201 MET A 202 LYS A 253 LYS A 257 SITE 2 BC1 6 PRO A 259 ASP A 313 SITE 1 BC2 4 LYS A 253 ALA A 254 ILE A 255 LYS A 257 SITE 1 BC3 3 TRP A 194 LYS A 195 GLU A 232 SITE 1 BC4 5 VAL A 112 GLU A 114 ALA A 254 HOH A 733 SITE 2 BC4 5 HOH A1135 CRYST1 84.120 84.120 166.270 90.00 90.00 90.00 P 42 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011888 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006014 0.00000