HEADER HYDROLASE 28-MAY-21 7EXW TITLE GH127 BETA-L-ARABINOFURANOSIDASE HYPBA1 COVALENTLY COMPLEXED WITH TITLE 2 ALPHA-L-ARABINOFURANOSYLAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-REDUCING END BETA-L-ARABINOFURANOSIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLYCOSIDE HYDROLASE; COMPND 5 SYNONYM: BETA-L-ARABINOFURANOSIDASE HYPBA1; COMPND 6 EC: 3.2.1.185; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM LONGUM SUBSP. LONGUM (STRAIN SOURCE 3 ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194B); SOURCE 4 ORGANISM_TAXID: 565042; SOURCE 5 STRAIN: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194B; SOURCE 6 GENE: HYPBA1, BLLJ_0211; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET23 KEYWDS (ALPHA/ALPHA)6 BARREL, GLYCOSIDE HYDROLASE FAMILY 127, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SAWANO,T.ARAKAWA,C.YAMADA,K.FUJITA,S.FUSHINOBU REVDAT 3 29-NOV-23 7EXW 1 REMARK REVDAT 2 30-MAR-22 7EXW 1 JRNL REVDAT 1 17-NOV-21 7EXW 0 JRNL AUTH S.MARUYAMA,K.SAWANO,S.AMAKI,T.SUZUKI,S.NARITA,K.KIMURA, JRNL AUTH 2 T.ARAKAWA,C.YAMADA,Y.ITO,N.DOHMAE,K.FUJITA,A.ISHIWATA, JRNL AUTH 3 S.FUSHINOBU JRNL TITL SUBSTRATE COMPLEX STRUCTURE, ACTIVE SITE LABELING AND JRNL TITL 2 CATALYTIC ROLE OF THE ZINC ION IN CYSTEINE GLYCOSIDASE. JRNL REF GLYCOBIOLOGY V. 32 171 2022 JRNL REFN ESSN 1460-2423 JRNL PMID 34735571 JRNL DOI 10.1093/GLYCOB/CWAB103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.ITO,K.SAIKAWA,S.KIM,K.FUJITA,A.ISHIWATA,S.KAEOTHIP, REMARK 1 AUTH 2 T.ARAKAWA,T.WKAGI,G.T.BECKHAM,Y.ITO,S.FUSHINOBU REMARK 1 TITL CRYSTAL STRUCTURE OF GLYCOSIDE HYDROLASE FAMILY 127 REMARK 1 TITL 2 BETA-L-ARABINOFURANOSIDASE FROM BIFIDOBACTERIUM LONGUM REMARK 1 REF BIOCHEMICAL AND BIOPHYSICAL V. 447 32 2014 REMARK 1 REF 2 RESEARCH COMMUNICATIONS REMARK 1 PMID 24680821 REMARK 1 DOI 10.1016/J.BBRC.2014.03.096 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 39895 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2025 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2932 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.59000 REMARK 3 B22 (A**2) : 1.59000 REMARK 3 B33 (A**2) : -5.17000 REMARK 3 B12 (A**2) : 0.80000 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.195 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.114 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5183 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4719 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7043 ; 1.495 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10842 ; 1.706 ; 1.584 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 641 ; 7.097 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;35.335 ;22.323 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 810 ;16.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;17.331 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5995 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1234 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7EXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42003 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.78200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3WKX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 M SODIUM CITRATE, 0.1 M MES-NAOH REMARK 280 (PH 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 168.03067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.01533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.01533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 168.03067 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: 5680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 VAL A 37 REMARK 465 PRO A 38 REMARK 465 ASP A 39 REMARK 465 ASP A 40 REMARK 465 PRO A 41 REMARK 465 ALA A 42 REMARK 465 GLY A 43 REMARK 465 ASN A 44 REMARK 465 GLN A 45 REMARK 465 LEU A 46 REMARK 465 ALA A 47 REMARK 465 ASP A 48 REMARK 465 ASP A 246 REMARK 465 LEU A 247 REMARK 465 ALA A 659 REMARK 465 ALA A 660 REMARK 465 ALA A 661 REMARK 465 LEU A 662 REMARK 465 GLU A 663 REMARK 465 HIS A 664 REMARK 465 HIS A 665 REMARK 465 HIS A 666 REMARK 465 HIS A 667 REMARK 465 HIS A 668 REMARK 465 HIS A 669 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 SG CYS A 415 CAH 09X A 801 1.56 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 ARG A 402 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 402 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 415 CB - CA - C ANGL. DEV. = 7.9 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 LEU A 137 59.26 -142.46 REMARK 500 HIS A 189 68.04 -107.10 REMARK 500 GLU A 196 -44.09 173.48 REMARK 500 ARG A 307 -13.65 -142.87 REMARK 500 ARG A 308 38.02 -149.51 REMARK 500 THR A 325 -81.77 -130.62 REMARK 500 TYR A 336 -60.79 -102.51 REMARK 500 ASN A 371 -84.19 -139.91 REMARK 500 TRP A 412 121.10 -173.06 REMARK 500 SER A 482 2.52 -62.50 REMARK 500 ALA A 483 -110.05 55.96 REMARK 500 THR A 484 -60.91 79.00 REMARK 500 ARG A 647 -148.75 -132.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 385 TYR A 386 147.93 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 A1083 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1084 DISTANCE = 6.21 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 09X A 801 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 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 338 OE2 REMARK 620 2 CYS A 340 SG 107.6 REMARK 620 3 CYS A 417 SG 97.3 107.8 REMARK 620 4 CYS A 418 SG 114.5 108.4 120.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7EXU RELATED DB: PDB REMARK 900 RELATED ID: 7EXV RELATED DB: PDB DBREF 7EXW A 1 658 UNP E8MGH8 HYBA1_BIFL2 1 658 SEQADV 7EXW ALA A 659 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW ALA A 660 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW ALA A 661 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW LEU A 662 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW GLU A 663 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 664 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 665 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 666 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 667 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 668 UNP E8MGH8 EXPRESSION TAG SEQADV 7EXW HIS A 669 UNP E8MGH8 EXPRESSION TAG SEQRES 1 A 669 MET ASN VAL THR ILE THR SER PRO PHE TRP LYS ARG ARG SEQRES 2 A 669 ARG ASP GLN ILE VAL GLU SER VAL ILE PRO TYR GLN TRP SEQRES 3 A 669 GLY VAL MET ASN ASP GLU ILE ASP THR THR VAL PRO ASP SEQRES 4 A 669 ASP PRO ALA GLY ASN GLN LEU ALA ASP SER LYS SER HIS SEQRES 5 A 669 ALA VAL ALA ASN LEU LYS VAL ALA ALA GLY GLU LEU ASP SEQRES 6 A 669 ASP GLU PHE HIS GLY MET VAL PHE GLN ASP SER ASP VAL SEQRES 7 A 669 TYR LYS TRP LEU GLU GLU ALA ALA TYR ALA LEU ALA TYR SEQRES 8 A 669 HIS PRO ASP PRO GLU LEU LYS ALA LEU CYS ASP ARG THR SEQRES 9 A 669 VAL ASP LEU ILE ALA ARG ALA GLN GLN SER ASP GLY TYR SEQRES 10 A 669 LEU ASP THR PRO TYR GLN ILE LYS SER GLY VAL TRP ALA SEQRES 11 A 669 ASP ARG PRO ARG PHE SER LEU ILE GLN GLN SER HIS GLU SEQRES 12 A 669 MET TYR VAL MET GLY HIS TYR ILE GLU ALA ALA VAL ALA SEQRES 13 A 669 TYR HIS GLN VAL THR GLY ASN GLU GLN ALA LEU GLU VAL SEQRES 14 A 669 ALA LYS LYS MET ALA ASP CYS LEU ASP ALA ASN PHE GLY SEQRES 15 A 669 PRO GLU GLU GLY LYS ILE HIS GLY ALA ASP GLY HIS PRO SEQRES 16 A 669 GLU ILE GLU LEU ALA LEU ALA LYS LEU TYR GLU GLU THR SEQRES 17 A 669 GLY GLU LYS ARG TYR LEU THR LEU SER GLN TYR LEU ILE SEQRES 18 A 669 ASP VAL ARG GLY GLN ASP PRO GLN PHE TYR ALA LYS GLN SEQRES 19 A 669 LEU LYS ALA MET ASN GLY ASP ASN ILE PHE HIS ASP LEU SEQRES 20 A 669 GLY PHE TYR LYS PRO THR TYR PHE GLN ALA ALA GLU PRO SEQRES 21 A 669 VAL ARG ASP GLN GLN THR ALA ASP GLY HIS ALA VAL ARG SEQRES 22 A 669 VAL GLY TYR LEU CYS THR GLY VAL ALA HIS VAL GLY ARG SEQRES 23 A 669 LEU LEU GLY ASP GLN GLY LEU ILE ASP THR ALA LYS ARG SEQRES 24 A 669 PHE TRP LYS ASN ILE VAL THR ARG ARG MET TYR VAL THR SEQRES 25 A 669 GLY ALA ILE GLY SER THR HIS VAL GLY GLU SER PHE THR SEQRES 26 A 669 TYR ASP TYR ASP LEU PRO ASN ASP THR MET TYR GLY GLU SEQRES 27 A 669 THR CYS ALA SER VAL ALA MET SER MET PHE ALA GLN GLN SEQRES 28 A 669 MET LEU ASP LEU GLU PRO LYS GLY GLU TYR ALA ASP VAL SEQRES 29 A 669 LEU GLU LYS GLU LEU PHE ASN GLY SER ILE ALA GLY ILE SEQRES 30 A 669 SER LEU ASP GLY LYS GLN TYR TYR TYR VAL ASN ALA LEU SEQRES 31 A 669 GLU THR THR PRO ASP GLY LEU ASP ASN PRO ASP ARG HIS SEQRES 32 A 669 HIS VAL LEU SER HIS ARG VAL ASP TRP PHE GLY CYS ALA SEQRES 33 A 669 CYS CYS PRO ALA ASN ILE ALA ARG LEU ILE ALA SER VAL SEQRES 34 A 669 ASP ARG TYR ILE TYR THR GLU ARG ASP GLY GLY LYS THR SEQRES 35 A 669 VAL LEU SER HIS GLN PHE ILE ALA ASN THR ALA GLU PHE SEQRES 36 A 669 ALA SER GLY LEU THR VAL GLU GLN ARG SER ASN PHE PRO SEQRES 37 A 669 TRP ASP GLY HIS VAL GLU TYR THR VAL SER LEU PRO ALA SEQRES 38 A 669 SER ALA THR ASP SER SER VAL ARG PHE GLY LEU ARG ILE SEQRES 39 A 669 PRO GLY TRP SER ARG GLY SER TYR THR LEU THR VAL ASN SEQRES 40 A 669 GLY LYS PRO ALA VAL GLY SER LEU GLU ASP GLY PHE VAL SEQRES 41 A 669 TYR LEU VAL VAL ASN ALA GLY ASP THR LEU GLU ILE ALA SEQRES 42 A 669 LEU GLU LEU ASP MET SER VAL LYS PHE VAL ARG ALA ASN SEQRES 43 A 669 SER ARG VAL ARG SER ASP ALA GLY GLN VAL ALA VAL MET SEQRES 44 A 669 ARG GLY PRO LEU VAL TYR CYS ALA GLU GLN VAL ASP ASN SEQRES 45 A 669 PRO GLY ASP LEU TRP ASN TYR ARG LEU ALA ASP GLY VAL SEQRES 46 A 669 THR GLY ALA ASP ALA ALA VAL ALA PHE GLN ALA ASP LEU SEQRES 47 A 669 LEU GLY GLY VAL ASP THR VAL ASP LEU PRO ALA VAL ARG SEQRES 48 A 669 GLU HIS ALA ASP GLU ASP ASP ALA PRO LEU TYR VAL ASP SEQRES 49 A 669 ALA ASP GLU PRO ARG ALA GLY GLU PRO ALA THR LEU ARG SEQRES 50 A 669 LEU VAL PRO TYR TYR SER TRP ALA ASN ARG GLU ILE GLY SEQRES 51 A 669 GLU MET ARG VAL PHE GLN ARG ARG ALA ALA ALA LEU GLU SEQRES 52 A 669 HIS HIS HIS HIS HIS HIS HET 09X A 801 13 HET ZN A 802 1 HETNAM 09X 2-BROMANYL-N-[(2R,3R,4R,5S}-5-(HYDROXYMETHYL)-3,4- HETNAM 2 09X BIS(OXIDANYL)OXOLAN-2-YL]ETHANAMIDE HETNAM ZN ZINC ION FORMUL 2 09X C7 H12 BR N O5 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *184(H2 O) HELIX 1 AA1 SER A 7 SER A 20 1 14 HELIX 2 AA2 SER A 20 ASN A 30 1 11 HELIX 3 AA3 HIS A 52 GLY A 62 1 11 HELIX 4 AA4 ASP A 75 HIS A 92 1 18 HELIX 5 AA5 ASP A 94 GLN A 112 1 19 HELIX 6 AA6 ASP A 119 LYS A 125 1 7 HELIX 7 AA7 SER A 126 ARG A 132 5 7 HELIX 8 AA8 LEU A 137 HIS A 142 1 6 HELIX 9 AA9 HIS A 142 GLY A 162 1 21 HELIX 10 AB1 ASN A 163 PHE A 181 1 19 HELIX 11 AB2 GLU A 196 GLY A 209 1 14 HELIX 12 AB3 GLU A 210 ARG A 224 1 15 HELIX 13 AB4 GLN A 229 MET A 238 1 10 HELIX 14 AB5 PRO A 260 GLN A 264 5 5 HELIX 15 AB6 HIS A 270 GLY A 289 1 20 HELIX 16 AB7 ASP A 290 ARG A 308 1 19 HELIX 17 AB8 HIS A 319 SER A 323 5 5 HELIX 18 AB9 GLU A 338 GLU A 356 1 19 HELIX 19 AC1 LYS A 358 ASN A 371 1 14 HELIX 20 AC2 SER A 373 ILE A 377 5 5 HELIX 21 AC3 THR A 393 ASN A 399 5 7 HELIX 22 AC4 ALA A 416 SER A 428 1 13 HELIX 23 AC5 VAL A 429 TYR A 432 5 4 HELIX 24 AC6 ASP A 438 GLY A 440 5 3 HELIX 25 AC7 PRO A 495 ARG A 499 5 5 HELIX 26 AC8 VAL A 549 ALA A 553 5 5 HELIX 27 AC9 ASP A 575 TRP A 577 5 3 HELIX 28 AD1 THR A 586 ALA A 590 5 5 HELIX 29 AD2 TYR A 642 TRP A 644 5 3 SHEET 1 AA1 7 ASN A 2 ILE A 5 0 SHEET 2 AA1 7 ASN A 451 GLU A 454 -1 O THR A 452 N THR A 4 SHEET 3 AA1 7 THR A 460 SER A 465 -1 O VAL A 461 N ALA A 453 SHEET 4 AA1 7 HIS A 472 SER A 478 -1 O GLU A 474 N ARG A 464 SHEET 5 AA1 7 THR A 529 GLU A 535 -1 O LEU A 534 N VAL A 473 SHEET 6 AA1 7 THR A 503 VAL A 506 -1 N THR A 503 O GLU A 535 SHEET 7 AA1 7 LYS A 509 PRO A 510 -1 O LYS A 509 N VAL A 506 SHEET 1 AA210 GLU A 391 THR A 392 0 SHEET 2 AA210 VAL A 540 VAL A 543 0 SHEET 3 AA210 GLN A 555 ARG A 560 -1 O MET A 559 N LYS A 541 SHEET 4 AA210 LEU A 563 GLU A 568 -1 O TYR A 565 N VAL A 558 SHEET 5 AA210 TYR A 579 LEU A 581 0 SHEET 6 AA210 ALA A 591 GLN A 595 0 SHEET 7 AA210 VAL A 602 GLU A 612 -1 O VAL A 602 N GLN A 595 SHEET 8 AA210 GLY A 631 PRO A 640 -1 O LEU A 636 N LEU A 607 SHEET 9 AA210 MET A 652 ARG A 653 -1 O ARG A 653 N ALA A 567 SHEET 10 AA210 GLN A 656 ARG A 657 1 O ARG A 657 N LEU A 581 SHEET 1 AA3 4 TYR A 434 ARG A 437 0 SHEET 2 AA3 4 THR A 442 SER A 445 -1 O LEU A 444 N THR A 435 SHEET 3 AA3 4 SER A 487 ARG A 493 1 O GLY A 491 N SER A 445 SHEET 4 AA3 4 PHE A 519 ASN A 525 -1 O LEU A 522 N PHE A 490 LINK OE2 GLU A 338 ZN ZN A 802 1555 1555 2.13 LINK SG CYS A 340 ZN ZN A 802 1555 1555 2.29 LINK SG CYS A 417 ZN ZN A 802 1555 1555 2.32 LINK SG CYS A 418 ZN ZN A 802 1555 1555 2.24 CISPEP 1 PHE A 467 PRO A 468 0 8.06 CRYST1 74.757 74.757 252.046 90.00 90.00 120.00 P 32 2 1 6 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 0.013377 0.007723 0.000000 0.00000 SCALE2 0.000000 0.015446 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003968 0.00000