HEADER SUGAR BINDING PROTEIN 25-NOV-08 3FDH TITLE CRYSTAL STRUCTURE OF A SUSD/RAGB FAMILY PROTEIN (BT_2033) FROM TITLE 2 BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUSD HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 GENE: BT_2033, NP_810946.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 30-OCT-24 3FDH 1 REMARK REVDAT 7 01-FEB-23 3FDH 1 REMARK SEQADV REVDAT 6 24-JUL-19 3FDH 1 REMARK LINK REVDAT 5 01-NOV-17 3FDH 1 REMARK REVDAT 4 13-JUL-11 3FDH 1 VERSN REVDAT 3 23-MAR-11 3FDH 1 TITLE KEYWDS REVDAT 2 24-NOV-09 3FDH 1 TITLE REVDAT 1 16-DEC-08 3FDH 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SUSD HOMOLOG (NP_810946.1) FROM JRNL TITL 2 BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58982 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2984 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4126 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 205 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3646 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 633 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.65000 REMARK 3 B22 (A**2) : 2.82000 REMARK 3 B33 (A**2) : -0.17000 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): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.864 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3787 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2511 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5148 ; 1.630 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6117 ; 1.527 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 3.983 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;33.376 ;24.757 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 599 ;11.208 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.229 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4341 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 790 ; 0.003 ; 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): 2371 ; 1.184 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 963 ; 0.265 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3797 ; 1.973 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1416 ; 3.472 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1343 ; 4.756 ; 8.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 39 A 157 REMARK 3 RESIDUE RANGE : A 168 A 520 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6668 34.4610 39.4628 REMARK 3 T TENSOR REMARK 3 T11: -0.0979 T22: -0.1245 REMARK 3 T33: -0.0930 T12: -0.0031 REMARK 3 T13: -0.0203 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 0.9400 L22: 0.5093 REMARK 3 L33: 0.8877 L12: 0.0796 REMARK 3 L13: -0.1100 L23: -0.0726 REMARK 3 S TENSOR REMARK 3 S11: 0.0178 S12: -0.1165 S13: 0.0131 REMARK 3 S21: 0.0433 S22: -0.0273 S23: -0.0206 REMARK 3 S31: 0.0118 S32: 0.0248 S33: 0.0095 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 RAMACHANDRAN OUTLIER RESIDUE 330 IS SUPPORTED BY DENSITY. 5. PEG- REMARK 3 200 MOLECULE FROM THE CRYO SOLUTION IS MODELED. REMARK 4 REMARK 4 3FDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050453. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-08 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 : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97871,0.97799 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58982 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.553 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 4.4490 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.68600 REMARK 200 R SYM FOR SHELL (I) : 0.68600 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30.0000% PEG-6000, 0.1M HEPES PH 7.0, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z 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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.92700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.35400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.48200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.92700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.35400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.48200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.92700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.35400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.48200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.92700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.35400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.48200 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 300 REMARK: AUTHORS STATE THAT RYSTAL PACKING ANALYSIS SUGGESTS THE REMARK 300 ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 ASP A 25 REMARK 465 THR A 26 REMARK 465 MSE A 27 REMARK 465 ASP A 28 REMARK 465 ARG A 29 REMARK 465 ILE A 30 REMARK 465 ASN A 31 REMARK 465 LYS A 32 REMARK 465 ASP A 33 REMARK 465 HIS A 34 REMARK 465 ASP A 35 REMARK 465 HIS A 36 REMARK 465 THR A 37 REMARK 465 THR A 38 REMARK 465 LEU A 158 REMARK 465 VAL A 159 REMARK 465 ASP A 160 REMARK 465 GLU A 161 REMARK 465 LYS A 162 REMARK 465 GLY A 163 REMARK 465 SER A 164 REMARK 465 PRO A 165 REMARK 465 VAL A 166 REMARK 465 TYR A 167 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 108 CE NZ REMARK 470 GLU A 119 CG CD OE1 OE2 REMARK 470 MSE A 168 CG SE CE REMARK 470 LYS A 311 CE NZ 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 ASN A 78 -136.15 53.80 REMARK 500 ASN A 88 -47.50 69.90 REMARK 500 CYS A 153 -68.63 -157.83 REMARK 500 LYS A 195 -137.64 -102.38 REMARK 500 ASN A 236 87.23 -159.22 REMARK 500 SER A 251 -151.50 -112.09 REMARK 500 SER A 330 33.74 -150.19 REMARK 500 SER A 334 144.54 -174.08 REMARK 500 ASN A 407 -157.12 -95.56 REMARK 500 VAL A 424 -52.87 -128.08 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 PG4 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 393011 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT (RESIDUE 23-520) WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3FDH A 23 520 UNP Q8A653 Q8A653_BACTN 23 520 SEQADV 3FDH GLY A 22 UNP Q8A653 EXPRESSION TAG SEQRES 1 A 499 GLY SER GLU ASP THR MSE ASP ARG ILE ASN LYS ASP HIS SEQRES 2 A 499 ASP HIS THR THR SER VAL ALA SER ARG PHE ILE LEU ALA SEQRES 3 A 499 ASP VAL ILE THR SER THR ALA PHE SER ASN ALA SER GLY SEQRES 4 A 499 ASP ILE ASN THR TYR ALA SER SER TYR ILE GLU TYR GLU SEQRES 5 A 499 VAL GLY VAL ASP ASN GLN LEU TYR TYR ALA GLU VAL ARG SEQRES 6 A 499 GLU ASN GLU PRO SER SER SER SER THR PHE ASN ASN SER SEQRES 7 A 499 TRP ASN GLY ILE TYR SER SER LEU LYS ASN ALA ARG ILE SEQRES 8 A 499 ILE ILE ASP GLN CYS GLY GLU GLY GLY ARG ASP HIS GLY SEQRES 9 A 499 ASN ASP VAL THR ARG GLY MSE ALA GLU VAL MSE ALA ALA SEQRES 10 A 499 TYR ASN CYS ALA LEU ILE ALA ASP PHE PHE GLY ASP ALA SEQRES 11 A 499 PRO CYS SER GLN ALA ALA LEU VAL ASP GLU LYS GLY SER SEQRES 12 A 499 PRO VAL TYR MSE THR PRO LYS MSE ASP THR GLN GLN GLU SEQRES 13 A 499 ILE TYR THR GLN ILE ILE SER TYR LEU ASP ASP ALA ILE SEQRES 14 A 499 ALA ASN LEU GLN LYS GLU ASP LEU ALA ASP VAL THR GLU SEQRES 15 A 499 GLN ASP PHE LEU TYR ALA GLY ASP ALA ASP LYS TRP LEU SEQRES 16 A 499 LYS PHE ALA TYR GLY LEU LYS ALA ARG TYR THR MSE ARG SEQRES 17 A 499 LEU ILE ASN ARG SER SER ASN LYS SER ALA ASP TYR GLU SEQRES 18 A 499 LYS VAL LEU ASP TYR VAL SER LYS SER PHE THR SER ALA SEQRES 19 A 499 ASP ASP GLN ALA ALA PHE ASP ILE TYR ASP SER ASN ASN SEQRES 20 A 499 ILE ASN PRO PHE TYR GLY PHE TYR ASN SER ARG ALA GLY SEQRES 21 A 499 PHE GLY ALA SER THR SER LEU GLY THR LYS LEU LEU ALA SEQRES 22 A 499 TYR ASN ASP PRO ARG ALA ASN ARG ALA PHE PHE THR PRO SEQRES 23 A 499 ILE VAL ASP LYS LYS ARG SER GLN VAL ALA ALA ASN ASP SEQRES 24 A 499 PRO SER LEU VAL PRO ALA PRO ASN GLY SER PRO ASP GLN SEQRES 25 A 499 SER THR SER LYS TYR GLY ILE SER ALA PHE VAL TYR ALA SEQRES 26 A 499 LYS THR ALA PRO THR LEU LEU MSE SER TYR HIS GLU LEU SEQRES 27 A 499 MSE PHE LEU LYS ALA GLU ALA LEU CYS ARG LEU ASN ARG SEQRES 28 A 499 ASP ALA GLU ASP ALA LEU LYS GLU ALA VAL VAL ALA GLY SEQRES 29 A 499 LEU LEU ASN ALA GLU ASN SER ILE SER ILE ALA ILE LYS SEQRES 30 A 499 GLU LEU GLY SER GLY LEU ASN THR ASN SER SER GLU VAL SEQRES 31 A 499 ILE THR GLU THR SER ALA GLY LYS TYR PHE ASP ASP VAL SEQRES 32 A 499 VAL LYS ALA LYS TYR ALA ALA ASN PRO LEU GLN GLU THR SEQRES 33 A 499 MSE ILE GLN LYS TYR LEU ALA MSE TRP GLY ALA SER GLY SEQRES 34 A 499 GLU ALA THR GLU THR TYR ASN ASP PHE ARG ARG MSE LYS SEQRES 35 A 499 GLY LEU ASN GLU ASN PHE ILE THR LEU THR ASN PRO ASN SEQRES 36 A 499 ASN SER SER LYS PHE PRO LEU ARG TYR PRO TYR GLY ASN SEQRES 37 A 499 SER ASP THR ALA ALA ASN PRO GLU VAL LYS ALA ALA TYR SEQRES 38 A 499 GLY ASN GLY ASP TYR VAL TYR SER GLU PRO VAL TRP TRP SEQRES 39 A 499 ALA GLY GLY SER ARG MODRES 3FDH MSE A 132 MET SELENOMETHIONINE MODRES 3FDH MSE A 136 MET SELENOMETHIONINE MODRES 3FDH MSE A 168 MET SELENOMETHIONINE MODRES 3FDH MSE A 172 MET SELENOMETHIONINE MODRES 3FDH MSE A 228 MET SELENOMETHIONINE MODRES 3FDH MSE A 354 MET SELENOMETHIONINE MODRES 3FDH MSE A 360 MET SELENOMETHIONINE MODRES 3FDH MSE A 438 MET SELENOMETHIONINE MODRES 3FDH MSE A 445 MET SELENOMETHIONINE MODRES 3FDH MSE A 462 MET SELENOMETHIONINE HET MSE A 132 8 HET MSE A 136 8 HET MSE A 168 5 HET MSE A 172 8 HET MSE A 228 8 HET MSE A 354 8 HET MSE A 360 8 HET MSE A 438 8 HET MSE A 445 8 HET MSE A 462 8 HET PG4 A 1 13 HETNAM MSE SELENOMETHIONINE HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 2 PG4 C8 H18 O5 FORMUL 3 HOH *633(H2 O) HELIX 1 1 ALA A 41 SER A 56 1 16 HELIX 2 2 GLY A 60 ILE A 70 1 11 HELIX 3 3 ASP A 77 VAL A 85 1 9 HELIX 4 4 ASN A 88 SER A 92 5 5 HELIX 5 5 PHE A 96 CYS A 117 1 22 HELIX 6 6 ASN A 126 GLY A 149 1 24 HELIX 7 7 THR A 174 LEU A 193 1 20 HELIX 8 8 ASP A 211 LEU A 230 1 20 HELIX 9 9 ILE A 231 SER A 234 5 4 HELIX 10 10 ASN A 236 LYS A 250 1 15 HELIX 11 11 SER A 254 GLN A 258 5 5 HELIX 12 12 ASN A 270 ALA A 280 1 11 HELIX 13 13 SER A 285 ASN A 296 1 12 HELIX 14 14 ASP A 297 ARG A 302 5 6 HELIX 15 15 ASP A 320 VAL A 324 5 5 HELIX 16 16 PHE A 343 ALA A 346 5 4 HELIX 17 17 SER A 355 LEU A 370 1 16 HELIX 18 18 ALA A 374 GLY A 401 1 28 HELIX 19 19 THR A 413 VAL A 424 1 12 HELIX 20 20 VAL A 424 ASN A 432 1 9 HELIX 21 21 ASN A 432 MSE A 445 1 14 HELIX 22 22 GLU A 451 LEU A 465 1 15 HELIX 23 23 ASN A 476 PHE A 481 1 6 HELIX 24 24 GLY A 488 ASN A 495 1 8 HELIX 25 25 ASN A 495 GLY A 503 1 9 HELIX 26 26 GLY A 505 SER A 510 5 6 HELIX 27 27 VAL A 513 GLY A 517 5 5 SHEET 1 A 2 GLU A 73 GLY A 75 0 SHEET 2 A 2 PHE A 282 ALA A 284 -1 O GLY A 283 N VAL A 74 SHEET 1 B 2 ALA A 151 PRO A 152 0 SHEET 2 B 2 MSE A 172 ASP A 173 -1 O ASP A 173 N ALA A 151 SHEET 1 C 2 ALA A 259 PHE A 261 0 SHEET 2 C 2 THR A 351 MSE A 354 -1 O THR A 351 N PHE A 261 SHEET 1 D 2 PHE A 304 PHE A 305 0 SHEET 2 D 2 ILE A 340 SER A 341 -1 O ILE A 340 N PHE A 305 SHEET 1 E 2 ARG A 313 SER A 314 0 SHEET 2 E 2 LEU A 404 ASN A 405 1 O ASN A 405 N ARG A 313 LINK C GLY A 131 N MSE A 132 1555 1555 1.32 LINK C MSE A 132 N ALA A 133 1555 1555 1.32 LINK C VAL A 135 N MSE A 136 1555 1555 1.32 LINK C MSE A 136 N ALA A 137 1555 1555 1.33 LINK C MSE A 168 N THR A 169 1555 1555 1.33 LINK C LYS A 171 N MSE A 172 1555 1555 1.32 LINK C MSE A 172 N ASP A 173 1555 1555 1.32 LINK C THR A 227 N MSE A 228 1555 1555 1.32 LINK C MSE A 228 N ARG A 229 1555 1555 1.33 LINK C LEU A 353 N MSE A 354 1555 1555 1.33 LINK C MSE A 354 N SER A 355 1555 1555 1.34 LINK C LEU A 359 N MSE A 360 1555 1555 1.31 LINK C MSE A 360 N PHE A 361 1555 1555 1.33 LINK C THR A 437 N MSE A 438 1555 1555 1.32 LINK C MSE A 438 N ILE A 439 1555 1555 1.34 LINK C ALA A 444 N MSE A 445 1555 1555 1.31 LINK C MSE A 445 N TRP A 446 1555 1555 1.32 LINK C ARG A 461 N MSE A 462 1555 1555 1.34 LINK C MSE A 462 N LYS A 463 1555 1555 1.33 SITE 1 AC1 7 PHE A 459 LYS A 463 GLU A 467 ASN A 468 SITE 2 AC1 7 ASN A 477 PHE A 481 HOH A1036 CRYST1 83.854 116.708 118.964 90.00 90.00 90.00 I 2 2 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 0.011926 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008406 0.00000 CONECT 723 725 CONECT 725 723 726 CONECT 726 725 727 729 CONECT 727 726 728 733 CONECT 728 727 CONECT 729 726 730 CONECT 730 729 731 CONECT 731 730 732 CONECT 732 731 CONECT 733 727 CONECT 749 754 CONECT 754 749 755 CONECT 755 754 756 758 CONECT 756 755 757 762 CONECT 757 756 CONECT 758 755 759 CONECT 759 758 760 CONECT 760 759 761 CONECT 761 760 CONECT 762 756 CONECT 909 910 CONECT 910 909 911 913 CONECT 911 910 912 914 CONECT 912 911 CONECT 913 910 CONECT 914 911 CONECT 930 937 CONECT 937 930 938 CONECT 938 937 939 941 CONECT 939 938 940 945 CONECT 940 939 CONECT 941 938 942 CONECT 942 941 943 CONECT 943 942 944 CONECT 944 943 CONECT 945 939 CONECT 1391 1396 CONECT 1396 1391 1397 CONECT 1397 1396 1398 1400 CONECT 1398 1397 1399 1404 CONECT 1399 1398 CONECT 1400 1397 1401 CONECT 1401 1400 1402 CONECT 1402 1401 1403 CONECT 1403 1402 CONECT 1404 1398 CONECT 2375 2381 CONECT 2381 2375 2382 CONECT 2382 2381 2383 2385 CONECT 2383 2382 2384 2389 CONECT 2384 2383 CONECT 2385 2382 2386 CONECT 2386 2385 2387 CONECT 2387 2386 2388 CONECT 2388 2387 CONECT 2389 2383 CONECT 2428 2434 CONECT 2434 2428 2435 CONECT 2435 2434 2436 2438 CONECT 2436 2435 2437 2442 CONECT 2437 2436 CONECT 2438 2435 2439 CONECT 2439 2438 2440 CONECT 2440 2439 2441 CONECT 2441 2440 CONECT 2442 2436 CONECT 3020 3025 CONECT 3025 3020 3026 CONECT 3026 3025 3027 3029 CONECT 3027 3026 3028 3033 CONECT 3028 3027 CONECT 3029 3026 3030 CONECT 3030 3029 3031 CONECT 3031 3030 3032 CONECT 3032 3031 CONECT 3033 3027 CONECT 3081 3084 CONECT 3084 3081 3085 CONECT 3085 3084 3086 3088 CONECT 3086 3085 3087 3092 CONECT 3087 3086 CONECT 3088 3085 3089 CONECT 3089 3088 3090 CONECT 3090 3089 3091 CONECT 3091 3090 CONECT 3092 3086 CONECT 3214 3223 CONECT 3223 3214 3224 CONECT 3224 3223 3225 3227 CONECT 3225 3224 3226 3231 CONECT 3226 3225 CONECT 3227 3224 3228 CONECT 3228 3227 3229 CONECT 3229 3228 3230 CONECT 3230 3229 CONECT 3231 3225 CONECT 3692 3693 CONECT 3693 3692 3694 CONECT 3694 3693 3695 CONECT 3695 3694 3696 CONECT 3696 3695 3697 CONECT 3697 3696 3698 CONECT 3698 3697 3699 CONECT 3699 3698 3700 CONECT 3700 3699 3701 CONECT 3701 3700 3702 CONECT 3702 3701 3703 CONECT 3703 3702 3704 CONECT 3704 3703 MASTER 366 0 11 27 10 0 2 6 4292 1 109 39 END