HEADER OXIDOREDUCTASE 04-APR-05 1Z9T TITLE CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI TITLE 2 AT 1.54 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL UPF0124 PROTEIN YFIH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YFIH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PUTATIVE LACCASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 9 06-NOV-24 1Z9T 1 REMARK REVDAT 8 15-NOV-23 1Z9T 1 REMARK REVDAT 7 20-SEP-23 1Z9T 1 REMARK REVDAT 6 25-JAN-23 1Z9T 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 1Z9T 1 VERSN REVDAT 4 28-JUL-10 1Z9T 1 HEADER TITLE KEYWDS REVDAT 3 24-FEB-09 1Z9T 1 VERSN REVDAT 2 03-MAY-05 1Z9T 1 REMARK REVDAT 1 12-APR-05 1Z9T 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL UPF0124 PROTEIN YFIH JRNL TITL 2 (NP_417084.1) FROM ESCHERICHIA COLI K12 AT 1.54 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42591 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2262 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3082 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.57000 REMARK 3 B22 (A**2) : -0.57000 REMARK 3 B33 (A**2) : 1.13000 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.087 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1935 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1767 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2597 ; 1.732 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4077 ; 1.447 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 238 ; 5.880 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;34.249 ;23.375 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;11.755 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.240 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2138 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 390 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 366 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1801 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 945 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1109 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 159 ; 0.143 ; 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): 7 ; 0.142 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.238 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.238 ; 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): 1261 ; 2.004 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 491 ; 0.474 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1901 ; 2.437 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 816 ; 4.358 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 695 ; 6.193 ;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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 243 REMARK 3 ORIGIN FOR THE GROUP (A): -11.7438 20.0477 2.7803 REMARK 3 T TENSOR REMARK 3 T11: -0.0599 T22: -0.0317 REMARK 3 T33: -0.0080 T12: -0.0136 REMARK 3 T13: 0.0089 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.0029 L22: 0.4629 REMARK 3 L33: 0.6086 L12: -0.3494 REMARK 3 L13: -0.3517 L23: 0.2194 REMARK 3 S TENSOR REMARK 3 S11: -0.0343 S12: 0.0688 S13: -0.0010 REMARK 3 S21: -0.0294 S22: -0.0136 S23: 0.0200 REMARK 3 S31: -0.0013 S32: -0.0449 S33: 0.0478 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 MASS SPEC ANALYSIS SHOWED THAT THE SE-METHIONINE INCORPATION RATE REMARK 3 WAS REMARK 3 ONLY 63% AND THE MODEL IS BUILT WITH THE OCCUPANCY OF THE SE ATOMS REMARK 3 IN REMARK 3 THE MSE RESIDUES AT 0.75 OCCUPANCY TO ACCOUNT FOR THE REDUCED REMARK 3 SCATTERING REMARK 3 POWER FROM THE 37% S-MET RESIDUES REMARK 4 REMARK 4 1Z9T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983967 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(311) BENT REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING); REMARK 200 SINGLE CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44917 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 60.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.75800 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1U05 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2HCITRATE, 20.0% PEG-3350, REMARK 280 NO BUFFER PH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.29450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.35550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.35550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.94175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.35550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.35550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.64725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.35550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.35550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.94175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.35550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.35550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.64725 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 45.29450 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 HIS A 0 REMARK 465 MSE A 1 REMARK 465 GLU A 81 REMARK 465 PRO A 82 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 GLN A 8 CD OE1 NE2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 LYS A 52 CE NZ REMARK 470 LYS A 63 CE NZ REMARK 470 LYS A 73 CE NZ REMARK 470 ARG A 160 NE CZ NH1 NH2 REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 GLU A 170 CG CD OE1 OE2 REMARK 470 LYS A 231 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 316 O HOH A 349 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 GLU A 119 CB GLU A 119 CG -0.122 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 34 59.42 -90.64 REMARK 500 ALA A 105 59.20 -158.62 REMARK 500 ASP A 106 -40.34 138.23 REMARK 500 ALA A 125 66.96 -114.30 REMARK 500 LYS A 231 -63.58 68.93 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 CIT A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 358298 RELATED DB: TARGETDB DBREF 1Z9T A 1 243 UNP P33644 YFIH_ECOLI 1 243 SEQADV 1Z9T MSE A -11 UNP P33644 EXPRESSION TAG SEQADV 1Z9T GLY A -10 UNP P33644 EXPRESSION TAG SEQADV 1Z9T SER A -9 UNP P33644 EXPRESSION TAG SEQADV 1Z9T ASP A -8 UNP P33644 EXPRESSION TAG SEQADV 1Z9T LYS A -7 UNP P33644 EXPRESSION TAG SEQADV 1Z9T ILE A -6 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A -5 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A -4 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A -3 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A -2 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A -1 UNP P33644 EXPRESSION TAG SEQADV 1Z9T HIS A 0 UNP P33644 EXPRESSION TAG SEQADV 1Z9T MSE A 1 UNP P33644 MET 1 MODIFIED RESIDUE SEQADV 1Z9T MSE A 103 UNP P33644 MET 103 MODIFIED RESIDUE SEQADV 1Z9T MSE A 173 UNP P33644 MET 173 MODIFIED RESIDUE SEQADV 1Z9T MSE A 236 UNP P33644 MET 236 MODIFIED RESIDUE SEQRES 1 A 255 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 255 SER LYS LEU ILE VAL PRO GLN TRP PRO GLN PRO LYS GLY SEQRES 3 A 255 VAL ALA ALA CYS SER SER THR ARG ILE GLY GLY VAL SER SEQRES 4 A 255 LEU PRO PRO TYR ASP SER LEU ASN LEU GLY ALA HIS CYS SEQRES 5 A 255 GLY ASP ASN PRO ASP HIS VAL GLU GLU ASN ARG LYS ARG SEQRES 6 A 255 LEU PHE ALA ALA GLY ASN LEU PRO SER LYS PRO VAL TRP SEQRES 7 A 255 LEU GLU GLN VAL HIS GLY LYS ASP VAL LEU LYS LEU THR SEQRES 8 A 255 GLY GLU PRO TYR ALA SER LYS ARG ALA ASP ALA SER TYR SEQRES 9 A 255 SER ASN THR PRO GLY THR VAL CYS ALA VAL MSE THR ALA SEQRES 10 A 255 ASP CYS LEU PRO VAL LEU PHE CYS ASN ARG ALA GLY THR SEQRES 11 A 255 GLU VAL ALA ALA ALA HIS ALA GLY TRP ARG GLY LEU CYS SEQRES 12 A 255 ALA GLY VAL LEU GLU GLU THR VAL SER CYS PHE ALA ASP SEQRES 13 A 255 ASN PRO GLU ASN ILE LEU ALA TRP LEU GLY PRO ALA ILE SEQRES 14 A 255 GLY PRO ARG ALA PHE GLU VAL GLY GLY GLU VAL ARG GLU SEQRES 15 A 255 ALA PHE MSE ALA VAL ASP ALA LYS ALA SER ALA ALA PHE SEQRES 16 A 255 ILE GLN HIS GLY ASP LYS TYR LEU ALA ASP ILE TYR GLN SEQRES 17 A 255 LEU ALA ARG GLN ARG LEU ALA ASN VAL GLY VAL GLU GLN SEQRES 18 A 255 ILE PHE GLY GLY ASP ARG CYS THR TYR THR GLU ASN GLU SEQRES 19 A 255 THR PHE PHE SER TYR ARG ARG ASP LYS THR THR GLY ARG SEQRES 20 A 255 MSE ALA SER PHE ILE TRP LEU ILE MODRES 1Z9T MSE A 103 MET SELENOMETHIONINE MODRES 1Z9T MSE A 173 MET SELENOMETHIONINE MODRES 1Z9T MSE A 236 MET SELENOMETHIONINE HET MSE A 103 9 HET MSE A 173 8 HET MSE A 236 8 HET CIT A 244 13 HET CIT A 245 13 HET EDO A 246 4 HET EDO A 247 4 HET EDO A 248 4 HET EDO A 249 4 HET EDO A 250 4 HET EDO A 251 4 HET EDO A 252 4 HET EDO A 253 4 HET EDO A 254 4 HET EDO A 255 4 HET EDO A 256 4 HET EDO A 257 4 HET EDO A 258 4 HET EDO A 259 4 HET EDO A 260 4 HET EDO A 261 4 HET EDO A 262 4 HET EDO A 263 4 HET EDO A 264 4 HETNAM MSE SELENOMETHIONINE HETNAM CIT CITRIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 CIT 2(C6 H8 O7) FORMUL 4 EDO 19(C2 H6 O2) FORMUL 23 HOH *218(H2 O) HELIX 1 1 ASN A 43 GLY A 58 1 16 HELIX 2 2 GLY A 126 GLY A 133 1 8 HELIX 3 3 GLY A 133 CYS A 141 1 9 HELIX 4 4 ASN A 145 GLU A 147 5 3 HELIX 5 5 GLY A 165 ASP A 176 1 12 HELIX 6 6 ALA A 177 ALA A 181 5 5 HELIX 7 7 ASP A 193 VAL A 205 1 13 HELIX 8 8 SER A 226 LYS A 231 1 6 SHEET 1 A 4 LEU A 4 ILE A 5 0 SHEET 2 A 4 VAL A 15 SER A 20 -1 O SER A 19 N ILE A 5 SHEET 3 A 4 MSE A 236 LEU A 242 -1 O PHE A 239 N CYS A 18 SHEET 4 A 4 VAL A 99 THR A 104 -1 N CYS A 100 O ILE A 240 SHEET 1 B 6 VAL A 75 LYS A 77 0 SHEET 2 B 6 ALA A 90 SER A 93 1 O ALA A 90 N LEU A 76 SHEET 3 B 6 VAL A 120 ALA A 125 -1 O VAL A 120 N SER A 93 SHEET 4 B 6 LEU A 108 ASN A 114 -1 N LEU A 108 O ALA A 125 SHEET 5 B 6 ILE A 149 LEU A 153 -1 O LEU A 150 N CYS A 113 SHEET 6 B 6 GLN A 209 GLY A 212 1 O PHE A 211 N LEU A 153 SHEET 1 C 3 GLU A 163 VAL A 164 0 SHEET 2 C 3 LYS A 189 ALA A 192 -1 O TYR A 190 N VAL A 164 SHEET 3 C 3 PHE A 183 HIS A 186 -1 N HIS A 186 O LYS A 189 LINK C VAL A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N THR A 104 1555 1555 1.32 LINK C PHE A 172 N MSE A 173 1555 1555 1.33 LINK C MSE A 173 N ALA A 174 1555 1555 1.32 LINK C ARG A 235 N MSE A 236 1555 1555 1.32 LINK C MSE A 236 N ALA A 237 1555 1555 1.33 CISPEP 1 PRO A 29 PRO A 30 0 8.51 CISPEP 2 ASP A 32 SER A 33 0 -1.90 SITE 1 AC1 8 ARG A 115 GLU A 163 VAL A 164 GLY A 165 SITE 2 AC1 8 LYS A 189 ARG A 228 EDO A 248 EDO A 264 SITE 1 AC2 11 HIS A 71 THR A 104 ALA A 105 ASP A 106 SITE 2 AC2 11 CYS A 107 HIS A 124 TYR A 227 ARG A 235 SITE 3 AC2 11 HOH A 281 HOH A 426 HOH A 470 SITE 1 AC3 6 LEU A 28 ASN A 43 HIS A 46 VAL A 205 SITE 2 AC3 6 HOH A 278 HOH A 348 SITE 1 AC4 7 ARG A 22 ILE A 23 GLY A 24 ASP A 32 SITE 2 AC4 7 SER A 33 GLU A 222 EDO A 253 SITE 1 AC5 5 PRO A 10 PRO A 12 ARG A 115 LYS A 189 SITE 2 AC5 5 CIT A 244 SITE 1 AC6 6 PRO A 159 ALA A 181 ALA A 182 ILE A 184 SITE 2 AC6 6 LEU A 191 GLN A 196 SITE 1 AC7 2 GLY A 58 HOH A 459 SITE 1 AC8 4 LEU A 67 GLN A 69 EDO A 257 HOH A 412 SITE 1 AC9 9 ASP A 106 CYS A 107 LEU A 108 ALA A 125 SITE 2 AC9 9 GLY A 126 TRP A 127 PHE A 162 ILE A 194 SITE 3 AC9 9 HOH A 407 SITE 1 BC1 4 ASP A 32 ASN A 221 EDO A 247 HOH A 333 SITE 1 BC2 6 ASP A 193 TYR A 195 ARG A 199 GLY A 213 SITE 2 BC2 6 EDO A 258 EDO A 263 SITE 1 BC3 6 VAL A 139 PHE A 142 ASP A 144 PRO A 146 SITE 2 BC3 6 HOH A 289 HOH A 404 SITE 1 BC4 1 ARG A 128 SITE 1 BC5 3 ARG A 51 EDO A 251 HOH A 279 SITE 1 BC6 4 PRO A 159 GLY A 213 ARG A 215 EDO A 254 SITE 1 BC7 6 TYR A 218 THR A 219 ASN A 221 ARG A 229 SITE 2 BC7 6 HOH A 305 HOH A 309 SITE 1 BC8 3 PRO A 44 ARG A 51 HOH A 334 SITE 1 BC9 4 GLU A 48 LYS A 52 HOH A 443 HOH A 454 SITE 1 CC1 4 PHE A 55 LEU A 60 SER A 62 HOH A 445 SITE 1 CC2 3 GLY A 212 GLY A 213 EDO A 254 SITE 1 CC3 6 TRP A 127 PHE A 162 ARG A 228 CIT A 244 SITE 2 CC3 6 HOH A 389 HOH A 398 CRYST1 80.711 80.711 90.589 90.00 90.00 90.00 P 43 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 0.012390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011040 0.00000