PDB Short entry for 2FFF HEADER MEMBRANE PROTEIN, TRANSFERASE 19-DEC-05 2FFF TITLE OPEN FORM OF A CLASS A TRANSPEPTIDASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 105-119; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: TRANSPEPTIDASE DOMAIN, RESIDUES 337-789; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 11 ORGANISM_TAXID: 1313; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS TRANSPEPTIDASE FOLD, MEMBRANE PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.L.LOVERING,N.C.J.STRYNADKA REVDAT 4 30-AUG-23 2FFF 1 REMARK LINK REVDAT 3 13-JUL-11 2FFF 1 VERSN REVDAT 2 24-FEB-09 2FFF 1 VERSN REVDAT 1 20-JUN-06 2FFF 0 JRNL AUTH A.L.LOVERING,L.DE CASTRO,D.LIM,N.C.STRYNADKA JRNL TITL STRUCTURAL ANALYSIS OF AN "OPEN" FORM OF PBP1B FROM JRNL TITL 2 STREPTOCOCCUS PNEUMONIAE. JRNL REF PROTEIN SCI. V. 15 1701 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16751607 JRNL DOI 10.1110/PS.062112106 REMARK 2 REMARK 2 RESOLUTION. 2.23 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27505 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1408 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) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1816 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 36.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : 1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.249 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.752 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3689 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3207 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5007 ; 1.326 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7482 ; 0.824 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 466 ; 6.826 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;33.344 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 606 ;14.863 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;14.442 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 549 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4180 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 728 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 851 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3213 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1777 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2006 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 190 ; 0.181 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.200 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.293 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.205 ; 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): 2982 ; 0.871 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 968 ; 0.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3704 ; 1.006 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1656 ; 1.574 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1303 ; 2.342 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 105 A 119 REMARK 3 RESIDUE RANGE : B 337 B 393 REMARK 3 RESIDUE RANGE : B 585 B 600 REMARK 3 ORIGIN FOR THE GROUP (A): 32.9602 8.9902 39.0669 REMARK 3 T TENSOR REMARK 3 T11: 0.0537 T22: 0.0583 REMARK 3 T33: -0.0573 T12: -0.0246 REMARK 3 T13: -0.0214 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.8830 L22: 0.9567 REMARK 3 L33: 0.8839 L12: -0.7917 REMARK 3 L13: -0.1993 L23: 0.5077 REMARK 3 S TENSOR REMARK 3 S11: -0.0147 S12: -0.1651 S13: -0.0273 REMARK 3 S21: 0.1442 S22: 0.0227 S23: 0.0267 REMARK 3 S31: 0.0205 S32: 0.0775 S33: -0.0080 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 394 B 584 REMARK 3 RESIDUE RANGE : B 601 B 789 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5403 6.9381 5.4629 REMARK 3 T TENSOR REMARK 3 T11: -0.0217 T22: -0.0239 REMARK 3 T33: -0.0139 T12: 0.0003 REMARK 3 T13: 0.0000 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.3350 L22: 0.1639 REMARK 3 L33: 0.3102 L12: 0.0763 REMARK 3 L13: 0.1283 L23: 0.0940 REMARK 3 S TENSOR REMARK 3 S11: 0.0210 S12: 0.0029 S13: 0.0026 REMARK 3 S21: 0.0186 S22: -0.0240 S23: 0.0085 REMARK 3 S31: 0.0076 S32: 0.0084 S33: 0.0030 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2FFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27505 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 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) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BG1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 20% PEG MME 2000, 10 MM REMARK 280 NICL2, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 65.83050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.02150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.83050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.02150 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 152 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE POLYPEPTIDE CHAINS A AND B ARE THE REGIONS OF THE REMARK 400 SAME CHIMERIC PROTEIN PROTEOLYSED TO TWO SEPARATE REMARK 400 SEGMENTS 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 ASP B 353 NE2 GLN B 357 2.09 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 B 456 NE - CZ - NH1 ANGL. DEV. = -3.7 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 GLN B 357 -61.62 -101.65 REMARK 500 ARG B 358 -87.44 -51.38 REMARK 500 ASP B 359 49.13 -66.80 REMARK 500 ASN B 360 -28.88 164.02 REMARK 500 LYS B 364 -16.63 -38.52 REMARK 500 GLU B 365 -25.03 -39.52 REMARK 500 ASN B 442 109.64 -166.35 REMARK 500 ALA B 459 -133.87 46.20 REMARK 500 ALA B 467 -76.17 -115.10 REMARK 500 ALA B 499 -120.90 54.84 REMARK 500 THR B 504 -102.96 -130.66 REMARK 500 ASN B 576 48.89 -85.93 REMARK 500 ASN B 640 83.29 -155.82 REMARK 500 SER B 708 75.94 -159.71 REMARK 500 GLU B 742 74.01 36.90 REMARK 500 LYS B 744 117.94 62.94 REMARK 500 ASN B 759 -155.51 -108.40 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 NI B 901 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 169 O REMARK 620 2 HIS B 682 ND1 88.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 901 DBREF 2FFF A 105 119 UNP Q4TUQ1 Q4TUQ1_STRPN 74 88 DBREF 2FFF B 337 789 UNP O70038 O70038_STRPN 337 789 SEQRES 1 A 15 ILE SER GLU ILE THR TYR SER ASP GLY THR VAL ILE ALA SEQRES 2 A 15 SER ILE SEQRES 1 B 453 ASP TYR LEU TYR PHE THR THR LEU ALA GLU ALA GLN GLU SEQRES 2 B 453 ARG MET TYR ASP TYR LEU ALA GLN ARG ASP ASN VAL SER SEQRES 3 B 453 ALA LYS GLU LEU LYS ASN GLU ALA THR GLN LYS PHE TYR SEQRES 4 B 453 ARG ASP LEU ALA ALA LYS GLU ILE GLU ASN GLY GLY TYR SEQRES 5 B 453 LYS ILE THR THR THR ILE ASP GLN LYS ILE HIS SER ALA SEQRES 6 B 453 MET GLN SER ALA VAL ALA ASP TYR GLY TYR LEU LEU ASP SEQRES 7 B 453 ASP GLY THR GLY ARG VAL GLU VAL GLY ASN VAL LEU MET SEQRES 8 B 453 ASP ASN GLN THR GLY ALA ILE LEU GLY PHE VAL GLY GLY SEQRES 9 B 453 ARG ASN TYR GLN GLU ASN GLN ASN ASN HIS ALA PHE ASP SEQRES 10 B 453 THR LYS ARG SER PRO ALA SER THR THR LYS PRO LEU LEU SEQRES 11 B 453 ALA TYR GLY ILE ALA ILE ASP GLN GLY LEU MET GLY SER SEQRES 12 B 453 GLU THR ILE LEU SER ASN TYR PRO THR ASN PHE ALA ASN SEQRES 13 B 453 GLY ASN PRO ILE MET TYR ALA ASN SER LYS GLY THR GLY SEQRES 14 B 453 MET MET THR LEU GLY GLU ALA LEU ASN TYR SER TRP ASN SEQRES 15 B 453 ILE PRO ALA TYR TRP THR TYR ARG MET LEU ARG GLU ASN SEQRES 16 B 453 GLY VAL ASP VAL LYS GLY TYR MET GLU LYS MET GLY TYR SEQRES 17 B 453 GLU ILE PRO GLU TYR GLY ILE GLU SER LEU PRO MET GLY SEQRES 18 B 453 GLY GLY ILE GLU VAL THR VAL ALA GLN HIS THR ASN GLY SEQRES 19 B 453 TYR GLN THR LEU ALA ASN ASN GLY VAL TYR HIS GLN LYS SEQRES 20 B 453 HIS VAL ILE SER LYS ILE GLU ALA ALA ASP GLY ARG VAL SEQRES 21 B 453 VAL TYR GLU TYR GLN ASP LYS PRO VAL GLN VAL TYR SER SEQRES 22 B 453 LYS ALA THR ALA THR ILE MET GLN GLY LEU LEU ARG GLU SEQRES 23 B 453 VAL LEU SER SER ARG VAL THR THR THR PHE LYS SER ASN SEQRES 24 B 453 LEU THR SER LEU ASN PRO THR LEU ALA ASN ALA ASP TRP SEQRES 25 B 453 ILE GLY LYS THR GLY THR THR ASN GLN ASP GLU ASN MET SEQRES 26 B 453 TRP LEU MET LEU SER THR PRO ARG LEU THR LEU GLY GLY SEQRES 27 B 453 TRP ILE GLY HIS ASP ASP ASN HIS SER LEU SER ARG ARG SEQRES 28 B 453 ALA GLY TYR SER ASN ASN SER ASN TYR MET ALA HIS LEU SEQRES 29 B 453 VAL ASN ALA ILE GLN GLN ALA SER PRO SER ILE TRP GLY SEQRES 30 B 453 ASN GLU ARG PHE ALA LEU ASP PRO SER VAL VAL LYS SER SEQRES 31 B 453 GLU VAL LEU LYS SER THR GLY GLN LYS PRO GLY LYS VAL SEQRES 32 B 453 SER VAL GLU GLY LYS GLU VAL GLU VAL THR GLY SER THR SEQRES 33 B 453 VAL THR SER TYR TRP ALA ASN LYS SER GLY ALA PRO ALA SEQRES 34 B 453 THR SER TYR ARG PHE ALA ILE GLY GLY SER ASP ALA ASP SEQRES 35 B 453 TYR GLN ASN ALA TRP SER SER ILE VAL GLY SER HET NI B 901 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI NI 2+ FORMUL 4 HOH *232(H2 O) HELIX 1 1 ASP B 337 ALA B 356 1 20 HELIX 2 2 ALA B 363 LYS B 367 5 5 HELIX 3 3 ASN B 368 GLY B 386 1 19 HELIX 4 4 ASP B 395 GLY B 410 1 16 HELIX 5 5 TYR B 411 ASP B 414 5 4 HELIX 6 6 PRO B 458 THR B 461 5 4 HELIX 7 7 THR B 462 ALA B 467 1 6 HELIX 8 8 ALA B 467 GLN B 474 1 8 HELIX 9 9 LEU B 509 SER B 516 1 8 HELIX 10 10 ASN B 518 ASN B 531 1 14 HELIX 11 11 ASP B 534 MET B 542 1 9 HELIX 12 12 SER B 553 GLY B 557 5 5 HELIX 13 13 THR B 563 ASN B 576 1 14 HELIX 14 14 SER B 609 ARG B 627 1 19 HELIX 15 15 THR B 631 ASN B 640 1 10 HELIX 16 16 ASN B 640 ASN B 645 1 6 HELIX 17 17 SER B 691 SER B 708 1 18 HELIX 18 18 SER B 775 GLY B 788 1 14 SHEET 1 A 5 VAL A 115 ILE A 119 0 SHEET 2 A 5 SER A 106 THR A 109 -1 N ILE A 108 O ILE A 116 SHEET 3 A 5 LYS B 389 THR B 392 1 O ILE B 390 N THR A 109 SHEET 4 A 5 ILE B 586 GLU B 590 -1 O GLU B 590 N LYS B 389 SHEET 5 A 5 VAL B 596 GLU B 599 -1 O TYR B 598 N ILE B 589 SHEET 1 B 5 ILE B 434 VAL B 438 0 SHEET 2 B 5 GLU B 421 ASP B 428 -1 N LEU B 426 O GLY B 436 SHEET 3 B 5 LEU B 670 GLY B 677 -1 O THR B 671 N MET B 427 SHEET 4 B 5 ASN B 660 SER B 666 -1 N LEU B 665 O LEU B 672 SHEET 5 B 5 ILE B 649 THR B 654 -1 N ILE B 649 O SER B 666 SHEET 1 C 2 ILE B 482 SER B 484 0 SHEET 2 C 2 MET B 506 THR B 508 -1 O MET B 507 N LEU B 483 SHEET 1 D 2 VAL B 579 TYR B 580 0 SHEET 2 D 2 VAL B 605 GLN B 606 -1 O VAL B 605 N TYR B 580 SHEET 1 E 2 VAL B 724 LEU B 729 0 SHEET 2 E 2 THR B 752 TRP B 757 -1 O SER B 755 N SER B 726 SHEET 1 F 2 GLY B 737 SER B 740 0 SHEET 2 F 2 GLU B 745 VAL B 748 -1 O VAL B 746 N VAL B 739 LINK O HOH B 169 NI NI B 901 1555 1555 2.73 LINK ND1 HIS B 682 NI NI B 901 1555 1555 1.75 SITE 1 AC1 4 HOH B 169 HOH B 183 THR B 417 HIS B 682 CRYST1 131.661 78.043 60.315 90.00 113.02 90.00 C 1 2 1 4 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 0.007590 0.000000 0.003230 0.00000 SCALE2 0.000000 0.012810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018010 0.00000