HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-DEC-04 1Y7M TITLE CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 A RESOLUTION CAVEAT 1Y7M CHIRALITY ERROR AT CHIRAL CENTER CA OF LEU 37A, ASN 30A,B. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN BSU14040; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: SUBSP. SUBTILIS STR. 168; SOURCE 5 GENE: YKUD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS SURFACE MUTAGENESIS, CYSTEINE PROTEASES, CELL WALL CATABOLISM, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.BIELNICKI,Y.DEVEDJIEV,U.DEREWENDA,Z.DAUTER,A.JOACHIMIAK, AUTHOR 2 Z.S.DEREWENDA,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 4 20-OCT-21 1Y7M 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1Y7M 1 VERSN REVDAT 2 12-APR-05 1Y7M 1 REMARK REVDAT 1 01-MAR-05 1Y7M 0 JRNL AUTH J.BIELNICKI,Y.DEVEDJIEV,U.DEREWENDA,Z.DAUTER,A.JOACHIMIAK, JRNL AUTH 2 Z.S.DEREWENDA JRNL TITL B. SUBTILIS YKUD PROTEIN AT 2.0 A RESOLUTION: INSIGHTS INTO JRNL TITL 2 THE STRUCTURE AND FUNCTION OF A NOVEL, UBIQUITOUS FAMILY OF JRNL TITL 3 BACTERIAL ENZYMES. JRNL REF PROTEINS V. 62 144 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 16287140 JRNL DOI 10.1002/PROT.20702 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20691 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1114 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.23000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : -2.48000 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): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.514 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2463 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2263 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3363 ; 1.441 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5241 ; 0.854 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 7.449 ; 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): 396 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2731 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 458 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 468 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2647 ; 0.237 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1524 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.189 ; 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): 21 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.225 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.204 ; 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): 1617 ; 0.548 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2605 ; 0.968 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 846 ; 1.872 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 758 ; 2.900 ; 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 1Y7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 77.3 REMARK 200 PH : 4.90 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946, 0.97919, 0.97178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21805 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, ACETATE, LITHIUM SULFATE, REMARK 280 CADMIUM CHLORIDE, PH 4.9, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294.1K, PH 4.90 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 28.13800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.83950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.95500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.83950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.13800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.95500 REMARK 290 SMTRY3 4 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: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LEU A 26 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 28 CD OE1 NE2 REMARK 480 ASN A 30 CB CG OD1 ND2 REMARK 480 PRO A 31 CB CG CD REMARK 480 LEU A 37 CB CG CD1 CD2 REMARK 480 GLN A 41 CG CD OE1 NE2 REMARK 480 SER A 42 CB OG REMARK 480 LYS A 85 CE NZ REMARK 480 ILE A 86 CD1 REMARK 480 GLN A 101 CD OE1 NE2 REMARK 480 ARG A 102 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 7 CD CE NZ REMARK 480 LEU B 26 CB CG CD1 CD2 REMARK 480 ASN B 30 CB CG OD1 ND2 REMARK 480 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 480 GLN B 101 CG CD OE1 NE2 REMARK 480 LYS B 145 CE NZ REMARK 480 ARG B 164 CG CD NE CZ NH1 NH2 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 OG SER B 22 O ALA B 25 1.22 REMARK 500 O LEU A 26 N ASN A 30 1.85 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 PRO A 31 C - N - CD ANGL. DEV. = -38.9 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 ALA A 25 92.17 -64.71 REMARK 500 LEU A 26 -40.78 86.24 REMARK 500 GLN A 34 89.88 -53.85 REMARK 500 ALA A 35 46.55 -152.24 REMARK 500 SER A 116 34.98 -73.77 REMARK 500 HIS A 119 -1.21 74.15 REMARK 500 GLN B 34 41.38 -79.94 REMARK 500 ALA B 35 55.04 -91.02 REMARK 500 SER B 116 34.22 -79.49 REMARK 500 HIS B 119 -3.62 80.21 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 LEU B 26 LEU B 27 -148.24 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 CD B 202 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 119 NE2 REMARK 620 2 CYS B 139 SG 122.1 REMARK 620 3 SO4 B 204 S 104.0 105.0 REMARK 620 4 SO4 B 204 O3 108.8 119.8 27.6 REMARK 620 5 SO4 B 204 O1 87.0 96.4 28.0 54.5 REMARK 620 6 HOH B 207 O 97.8 115.0 112.7 85.0 138.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 201 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 139 SG REMARK 620 2 SO4 A 203 O4 115.9 REMARK 620 3 SO4 A 203 O2 101.6 54.0 REMARK 620 4 SO4 A 203 S 105.0 27.6 27.7 REMARK 620 5 HOH A 204 O 111.0 84.8 136.0 112.4 REMARK 620 6 HIS B 119 NE2 121.9 115.8 88.2 108.4 98.2 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 CD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC1283 RELATED DB: TARGETDB DBREF 1Y7M A 1 164 UNP O34816 O34816_BACSU 1 164 DBREF 1Y7M B 1 164 UNP O34816 O34816_BACSU 1 164 SEQADV 1Y7M MSE A 1 UNP O34816 MET 1 MODIFIED RESIDUE SEQADV 1Y7M MSE A 76 UNP O34816 MET 76 MODIFIED RESIDUE SEQADV 1Y7M ALA A 117 UNP O34816 LYS 117 ENGINEERED MUTATION SEQADV 1Y7M ALA A 118 UNP O34816 GLN 118 ENGINEERED MUTATION SEQADV 1Y7M MSE A 142 UNP O34816 MET 142 MODIFIED RESIDUE SEQADV 1Y7M MSE B 1 UNP O34816 MET 1 MODIFIED RESIDUE SEQADV 1Y7M MSE B 76 UNP O34816 MET 76 MODIFIED RESIDUE SEQADV 1Y7M ALA B 117 UNP O34816 LYS 117 ENGINEERED MUTATION SEQADV 1Y7M ALA B 118 UNP O34816 GLN 118 ENGINEERED MUTATION SEQADV 1Y7M MSE B 142 UNP O34816 MET 142 MODIFIED RESIDUE SEQRES 1 A 164 MSE LEU THR TYR GLN VAL LYS GLN GLY ASP THR LEU ASN SEQRES 2 A 164 SER ILE ALA ALA ASP PHE ARG ILE SER THR ALA ALA LEU SEQRES 3 A 164 LEU GLN ALA ASN PRO SER LEU GLN ALA GLY LEU THR ALA SEQRES 4 A 164 GLY GLN SER ILE VAL ILE PRO GLY LEU PRO ASP PRO TYR SEQRES 5 A 164 THR ILE PRO TYR HIS ILE ALA VAL SER ILE GLY ALA LYS SEQRES 6 A 164 THR LEU THR LEU SER LEU ASN ASN ARG VAL MSE LYS THR SEQRES 7 A 164 TYR PRO ILE ALA VAL GLY LYS ILE LEU THR GLN THR PRO SEQRES 8 A 164 THR GLY GLU PHE TYR ILE ILE ASN ARG GLN ARG ASN PRO SEQRES 9 A 164 GLY GLY PRO PHE GLY ALA TYR TRP LEU SER LEU SER ALA SEQRES 10 A 164 ALA HIS TYR GLY ILE HIS GLY THR ASN ASN PRO ALA SER SEQRES 11 A 164 ILE GLY LYS ALA VAL SER LYS GLY CYS ILE ARG MSE HIS SEQRES 12 A 164 ASN LYS ASP VAL ILE GLU LEU ALA SER ILE VAL PRO ASN SEQRES 13 A 164 GLY THR ARG VAL THR ILE ASN ARG SEQRES 1 B 164 MSE LEU THR TYR GLN VAL LYS GLN GLY ASP THR LEU ASN SEQRES 2 B 164 SER ILE ALA ALA ASP PHE ARG ILE SER THR ALA ALA LEU SEQRES 3 B 164 LEU GLN ALA ASN PRO SER LEU GLN ALA GLY LEU THR ALA SEQRES 4 B 164 GLY GLN SER ILE VAL ILE PRO GLY LEU PRO ASP PRO TYR SEQRES 5 B 164 THR ILE PRO TYR HIS ILE ALA VAL SER ILE GLY ALA LYS SEQRES 6 B 164 THR LEU THR LEU SER LEU ASN ASN ARG VAL MSE LYS THR SEQRES 7 B 164 TYR PRO ILE ALA VAL GLY LYS ILE LEU THR GLN THR PRO SEQRES 8 B 164 THR GLY GLU PHE TYR ILE ILE ASN ARG GLN ARG ASN PRO SEQRES 9 B 164 GLY GLY PRO PHE GLY ALA TYR TRP LEU SER LEU SER ALA SEQRES 10 B 164 ALA HIS TYR GLY ILE HIS GLY THR ASN ASN PRO ALA SER SEQRES 11 B 164 ILE GLY LYS ALA VAL SER LYS GLY CYS ILE ARG MSE HIS SEQRES 12 B 164 ASN LYS ASP VAL ILE GLU LEU ALA SER ILE VAL PRO ASN SEQRES 13 B 164 GLY THR ARG VAL THR ILE ASN ARG MODRES 1Y7M MSE A 1 MET SELENOMETHIONINE MODRES 1Y7M MSE A 76 MET SELENOMETHIONINE MODRES 1Y7M MSE A 142 MET SELENOMETHIONINE MODRES 1Y7M MSE B 1 MET SELENOMETHIONINE MODRES 1Y7M MSE B 76 MET SELENOMETHIONINE MODRES 1Y7M MSE B 142 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 76 8 HET MSE A 142 8 HET MSE B 1 8 HET MSE B 76 8 HET MSE B 142 8 HET CD A 201 1 HET SO4 A 203 5 HET CD B 202 1 HET SO4 B 204 5 HET SO4 B 205 5 HET SO4 B 206 5 HETNAM MSE SELENOMETHIONINE HETNAM CD CADMIUM ION HETNAM SO4 SULFATE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 CD 2(CD 2+) FORMUL 4 SO4 4(O4 S 2-) FORMUL 9 HOH *156(H2 O) HELIX 1 1 THR A 11 PHE A 19 1 9 HELIX 2 2 ASP A 50 ILE A 54 5 5 HELIX 3 3 GLY A 105 GLY A 109 5 5 HELIX 4 4 ASN A 127 ILE A 131 5 5 HELIX 5 5 HIS A 143 VAL A 154 1 12 HELIX 6 6 THR B 11 PHE B 19 1 9 HELIX 7 7 ASP B 50 ILE B 54 5 5 HELIX 8 8 GLY B 105 GLY B 109 5 5 HELIX 9 9 ASN B 127 ILE B 131 5 5 HELIX 10 10 HIS B 143 VAL B 154 1 12 SHEET 1 A 2 LEU A 2 GLN A 5 0 SHEET 2 A 2 SER A 42 ILE A 45 -1 O ILE A 43 N TYR A 4 SHEET 1 B 8 ARG A 74 PRO A 80 0 SHEET 2 B 8 THR A 66 LEU A 71 -1 N LEU A 69 O MSE A 76 SHEET 3 B 8 TYR A 56 SER A 61 -1 N ALA A 59 O THR A 68 SHEET 4 B 8 ARG A 159 ASN A 163 1 O ARG A 159 N ILE A 58 SHEET 5 B 8 GLY A 93 ARG A 102 -1 N PHE A 95 O VAL A 160 SHEET 6 B 8 TYR A 111 LEU A 115 -1 O SER A 114 N ILE A 98 SHEET 7 B 8 GLY A 121 HIS A 123 -1 O ILE A 122 N LEU A 113 SHEET 8 B 8 ILE A 140 ARG A 141 1 O ILE A 140 N HIS A 123 SHEET 1 C 2 VAL A 83 GLY A 84 0 SHEET 2 C 2 ALA A 134 SER A 136 1 O SER A 136 N VAL A 83 SHEET 1 D 2 LEU B 2 GLN B 5 0 SHEET 2 D 2 SER B 42 ILE B 45 -1 O ILE B 45 N LEU B 2 SHEET 1 E 8 ARG B 74 PRO B 80 0 SHEET 2 E 8 THR B 66 LEU B 71 -1 N LEU B 69 O MSE B 76 SHEET 3 E 8 TYR B 56 SER B 61 -1 N ALA B 59 O THR B 68 SHEET 4 E 8 ARG B 159 ASN B 163 1 O THR B 161 N VAL B 60 SHEET 5 E 8 GLY B 93 ARG B 102 -1 N GLY B 93 O ILE B 162 SHEET 6 E 8 TYR B 111 LEU B 115 -1 O SER B 114 N ILE B 98 SHEET 7 E 8 GLY B 121 HIS B 123 -1 O ILE B 122 N LEU B 113 SHEET 8 E 8 ILE B 140 ARG B 141 1 O ILE B 140 N HIS B 123 SHEET 1 F 2 VAL B 83 GLY B 84 0 SHEET 2 F 2 ALA B 134 SER B 136 1 O SER B 136 N VAL B 83 LINK C MSE A 1 N LEU A 2 1555 1555 1.34 LINK C VAL A 75 N MSE A 76 1555 1555 1.33 LINK C MSE A 76 N LYS A 77 1555 1555 1.33 LINK C ARG A 141 N MSE A 142 1555 1555 1.33 LINK C MSE A 142 N HIS A 143 1555 1555 1.34 LINK C MSE B 1 N LEU B 2 1555 1555 1.34 LINK C VAL B 75 N MSE B 76 1555 1555 1.32 LINK C MSE B 76 N LYS B 77 1555 1555 1.34 LINK C ARG B 141 N MSE B 142 1555 1555 1.33 LINK C MSE B 142 N HIS B 143 1555 1555 1.33 LINK NE2 HIS A 119 CD CD B 202 4455 1555 2.33 LINK SG CYS A 139 CD CD A 201 1555 1555 2.33 LINK CD CD A 201 O4 SO4 A 203 1555 1555 2.76 LINK CD CD A 201 O2 SO4 A 203 1555 1555 2.57 LINK CD CD A 201 S SO4 A 203 1555 1555 3.14 LINK CD CD A 201 O HOH A 204 1555 1555 2.66 LINK CD CD A 201 NE2 HIS B 119 1555 4555 2.27 LINK SG CYS B 139 CD CD B 202 1555 1555 2.34 LINK CD CD B 202 S SO4 B 204 1555 1555 3.12 LINK CD CD B 202 O3 SO4 B 204 1555 1555 2.52 LINK CD CD B 202 O1 SO4 B 204 1555 1555 2.70 LINK CD CD B 202 O HOH B 207 1555 1555 2.62 CISPEP 1 ALA B 25 LEU B 26 0 10.45 SITE 1 AC1 4 CYS A 139 SO4 A 203 HOH A 204 HIS B 119 SITE 1 AC2 4 HIS A 119 CYS B 139 SO4 B 204 HOH B 207 SITE 1 AC3 8 HIS A 123 SER A 136 LYS A 137 GLY A 138 SITE 2 AC3 8 CYS A 139 ARG A 141 CD A 201 HIS B 119 SITE 1 AC4 8 HIS A 119 HIS B 123 SER B 136 LYS B 137 SITE 2 AC4 8 GLY B 138 CYS B 139 ARG B 141 CD B 202 SITE 1 AC5 4 ARG A 159 HOH A 238 TYR B 96 ARG B 159 SITE 1 AC6 4 ASN A 144 LYS B 145 HOH B 211 HOH B 225 CRYST1 56.276 63.910 93.679 90.00 90.00 90.00 P 21 21 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 0.017770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015647 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010675 0.00000 HETATM 1 N MSE A 1 69.374 15.949 21.053 1.00 32.28 N HETATM 2 CA MSE A 1 68.140 15.103 20.970 1.00 32.57 C HETATM 3 C MSE A 1 67.456 15.106 19.582 1.00 30.00 C HETATM 4 O MSE A 1 66.674 14.202 19.304 1.00 29.16 O HETATM 5 CB MSE A 1 67.110 15.468 22.071 1.00 33.88 C HETATM 6 CG MSE A 1 67.683 15.956 23.409 1.00 39.70 C HETATM 7 SE MSE A 1 67.222 14.789 24.969 1.00 55.27 SE HETATM 8 CE MSE A 1 68.913 15.024 26.088 1.00 52.41 C